Genomic comparison of Staphylococcus aureus isolates from patients with bacteraemia and infective endocarditis at public hospitals in Gauteng, South Africa

Genomic comparison of Staphylococcus aureus isolates from patients with bacteraemia and infective endocarditis at public hospitals in Gauteng, South Africa | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Genomic comparison of Staphylococcus aureus isolates from patients with bacteraemia and infective endocarditis at public hospitals in Gauteng, South Africa Lz D. Spaltman, Thabo Hamiwe, Veronica Ueckermann, Marleen M. Kock, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8678564/v1 This work is licensed under a CC BY 4.0 License Status: Under Revision Version 1 posted 9 You are reading this latest preprint version Abstract Staphylococcus aureus ( S. aureus ) is a leading cause of bacteraemia and infective endocarditis worldwide, posing significant public health challenges in resource-limited low- and middle-income countries (LMICs). However, whether specific genomic factors influence S. aureus infective endocarditis (SAIE) development during S. aureus bacteraemia (SAB) remains unclear. Thus, the study aimed to determine whether clinical SAIE isolates were genomically distinguishable from SAB isolates originating from public hospitals in Gauteng, South Africa. Seventy-seven (54 SAB, 23 SAIE) bloodstream isolates were characterised to assess antimicrobial susceptibility (VITEK ® 2 system), biofilm formation (crystal violet assay), virulence genes (multiplex-polymerase chain reactions) and genetic relatedness (pulsed-field gel electrophoresis). Twelve representative isolates underwent whole-genome sequencing to assess their mobilome, resistome, virulome and phylogenetic relatedness. A higher SAIE (29.9%) prevalence than previously reported in South Africa was observed, with cases linked to young male persons who inject drugs (P < 0.01). While SAB and SAIE groups did not differ in virulence profiles, SAB cases demonstrated higher resistance rates to gentamicin and clindamycin compared to SAIE (P < 0.05). The endemic Panton-Valentine leukocidin-positive sequence-type (ST) 152, clonal-complex (CC) 152 lineage predominated in SAIE isolates, while the pandemic CC8, encompassing ST239, ST508 and ST612, was exclusive to SAB isolates. The findings suggest that all SAB isolates may be capable of progressing to more severe SAIE forms with host risk factors as key predictors. Circulation of diverse, highly pathogenic S. aureus strains highlights the need for surveillance and targeted infection control. bacteraemia genetic relatedness infective endocarditis Staphylococcus aureus virulence Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 INTRODUCTION Staphylococcus aureus ( S. aureus ) remains a formidable threat to human health and well-being and is a leading cause of bacteraemia and infective endocarditis (IE) worldwide (Agnello et al., 2021 ). While often transient, unresolved S. aureus bacteraemia (SAB) infections can progress to severe complications, including S. aureus IE (SAIE), a rare yet deadly localised endocardial infection with high rates of recurrence (Kinney et al., 2022a ). The emergence of SAIE has become particularly pronounced in South Africa (SA) and is the leading cause of IE among persons who inject drugs (PWIDs) (Pecoraro et al., 2021 ). With a high proportion of the SA population at risk due to immunocompromising conditions and limited access to quality healthcare, S. aureus poses a significant public health concern (Achoki et al., 2022 ). Despite its clinical significance, the characteristics, outcome-related factors and local epidemiology of SAIE in SA healthcare-associated (HA) settings remain underexplored. The pathogenic success of S. aureus arises from extensive antimicrobial resistance (AMR) mechanisms and virulence factors that facilitate host colonisation, immune evasion and persistence (Kinney et al., 2022a ). Cardiac vegetation formation, pathognomonic of SAIE, is promoted by adhesins and coagulases that trigger platelet activation and aggregation, including clumping factor A (ClfA), fibronectin-binding protein A (FnBPA), iron-regulated surface determinant protein B (IsdB), serine-aspartate repeat-containing protein E (SdrE), extracellular adherence protein (Eap), coagulase (Coa) and von Willebrand factor-binding protein (vWbp) (Kinney et al., 2022b ). Whereas exoenzymes, haemolysins and superantigens (SAgs) drive the aggressive nature of SAIE (Kinney et al., 2022a ). Specific toxins, including beta (β)-haemolysin (Hlb), staphylococcal enterotoxin (SE) C (SEC), the enterotoxin gene cluster [ egc ; SEI, SEM, SEO, SE-like toxin U (SEl-U)] and toxic shock syndrome toxin-1 (TSST-1) are thought to induce disease by altering endothelial cell activity and promoting vegetation (Kinney et al., 2022b ). Additionally, SAgs affect SAIE progression by dysregulating immune responses, causing persistent inflammation and cytotoxicity (Salgado-Pabón et al., 2013 ). The present study was prompted by conflicting evidence on the distinguishability between SAB and SAIE strains. Earlier studies (Salgado-Pabón et al., 2013 ; Bouchiat et al., 2015 ) suggested certain bacterial phenotypes might be linked to SAIE, whereas a recent multi-high-income country (HIC) study (Bastien et al., 2023 ) found similar pathogenic potential across all SAB and SAIE strains. However, given the absence of African isolates, limited local genomic surveillance and contextual differences between SA and the HICs assessed, whether local strain characteristics follow these trends remained unclear, warranting region-specific investigation. Therefore, this study aimed to characterise S. aureus isolates associated with SAB and SAIE cases at Gauteng public hospitals to determine whether clinical SAIE isolates are genomically distinguishable from non-IE SAB isolates or whether specific factors influence the progression to SAIE. MATERIALS AND METHODS Study setting and collection of S. aureus isolates Ethical approval for the study was obtained from the University of Pretoria (UP), Faculty of Health Sciences Research Ethics Committee (Reference number: 183/2023). The study was conducted at the Department of Medical Microbiology, UP, using S. aureus isolates collected between February and November 2023 from a public diagnostic laboratory in Tshwane, SA. This diagnostic laboratory provides services to public clinics and hospitals at both primary and tertiary levels within the city of Tshwane and surrounding areas. The S. aureus isolates were collected from cases of bloodstream infections after routine diagnostic specimen processing, which included species identification and antimicrobial susceptibility testing (AST) using the VITEK ® 2 system (bioMérieux, France). Patient demographic, epidemiological, clinical and microbiological data were retrospectively collected from diagnostic laboratory databases and patient records. Isolate infection type (SAB or SAIE) was assigned based on the patient’s final clinical diagnosis, with the assistance of a clinician. Molecular species confirmation and virulence characterisation Seventy-seven non-repeat S. aureus bloodstream isolates were streaked onto 5% sheep blood agar (MediaMage, SA) and incubated for 24 h at 37°C (Vacutec, UK). Thereafter, a single pure colony was inoculated into 5 mL sterile Brain Heart Infusion broth (LabM, UK) and incubated with shaking (Stuart Orbital Incubator, UK) for 24 h at 37°C. Total genomic DNA extraction was performed following the boiling method, with modifications (Barbosa et al., 2016). Briefly, phosphate-buffered saline [PBS, pH 7.2 (Thermo Scientific, USA)] was used instead of a detergent-based lysis buffer. Cultures were centrifuged three times (MC-24 ® Touch, Benchmark, USA): initially at 5,500 × g for 5 s, followed by two additional centrifugation and PBS (Thermo Scientific, USA) wash steps at 5,500 × g for 5 min. Lastly, a sonication step (Transsonic 460, USA) of 15 min at 35 kHz was incorporated to improve cell lysis. A species identification multiplex polymerase chain reaction (M-PCR) assay was performed to confirm isolates as S. aureus and to differentiate methicillin-resistant S. aureus (MRSA) from methicillin-sensitive S. aureus (MSSA) based on the presence of the methicillin-resistance gene ( mecA ). The S. aureus isolates were screened for multiple virulence genes previously associated with SAIE, including cytolytic toxins, exoenzymes, regulatory elements, SAgs, secretable expanded repertoire adhesive molecules (SERAMs) and microbial surface components recognising adhesive matrix molecules (MSCRAMMs). Primer sequences and amplification conditions used in the conventional M-PCR assays are indicated in Table S1 provided in Online Resource 1. A CelTaq Hotstart DNA polymerase and buffer (Celtic Molecular Diagnostics, SA) master mix was prepared according to the manufacturer’s instructions. The S. aureus ATCC 33591, 29213, 700699, 25923, 24213 and in-house controls were used in the identification and virulence gene detection M-PCR assays, with results interpreted according to expected amplicon band sizes for each target gene, as detailed in Table S1 in Online Resource 1. Evaluation of S. aureus phenotypic biofilm formation Biofilm formation was assessed using the crystal violet assay as previously described (Merritt et al., 2005), with modifications that included culturing in 1% glucose-supplemented tryptic soy broth (Oxoid, UK), heat fixation (ProBlot 12S, Labnet, USA) at 65°C for 1 h prior to staining and the use of PBS (Thermo Scientific, USA) for washing. The S. aureus ATCC 12600 was included as a reference strain. Biofilm biomass was quantified by measuring the optical density (OD) at 550 nm (OD₅₅₀) using a PR 4100 Absorbance Microtiter Plate Reader (BioRad, USA). The OD was measured using the following formula: OD cut-off (ODc) = Average OD of negative control + [3 × standard deviation (SD) of the negative control]. The final OD used to characterise biofilm formation was calculated as average isolate OD – ODc. Isolates were categorised as non (OD ≤ ODc), weak (ODc < OD ≤ 2 × ODc), moderate (2 × ODc < OD ≤ 4 × ODc) or strong (4 × ODc < OD) biofilm formers. Pulsed-field gel electrophoresis genotyping The genetic relatedness of the S. aureus isolates was assessed using pulsed-field gel electrophoresis (PFGE) with the S. aureus ATCC 12600 strain as a size standard. Plug preparation was done according to McDougal et al. (2003) and the CHEF-DR ® III protocol (BioRad, USA). Genomic DNA was digested with SmaI (Thermo Scientific, USA) and resolved on a 1.2% (m/v) Seakem agarose gel (Lonza, USA) stained with ethidium bromide [250 μL of 10 mg/mL (Sigma-Aldrich, USA)]. The run conditions were as follows: 21 h at 14°C with an interval of 5-40 s linear at a constant angle of 120° and a voltage of 200-220 V. Gel images were analysed using GelCompar II (Applied Maths, Belgium) with cluster analysis performed using the Dice coefficient and the dendrogram constructed using unweighted pair group method with arithmetic mean. An ≥80% similarity threshold was used to define and categorise pulsotypes as major (≥5 isolates), minor (<5 isolates) or singletons. Whole genome sequencing of selected S. aureus isolates Due to the high cost of whole-genome sequencing (WGS) in SA, only 12 representative S. aureus isolates (6 SAB, 6 SAIE) were selected for this analysis. The selection aimed to capture phenotypic and genotypic diversity. Thus, isolates were considered based on AST profiles [fully susceptible to multidrug resistance (MDR)], number of virulence genes detected (low to high), biofilm-forming capacity (none to strong), patient outcome (a fatal case) and PFGE clustering to represent major clusters, minor clusters, singletons and one untypable isolate. The Quick-DNA TM Fungal/Bacterial Miniprep Kit (Zymo Research, USA) was used for DNA extraction according to the manufacturer’s instructions. The DNA quality (A260/A280 ≥1.8) was verified using a nano spectrophotometer (Labtron, UK) and submitted to the National Institute for Communicable Diseases (NICD), SA, for WGS. Multiplexed, paired-end libraries were prepared using the Nextera DNA Flex Kit (Illumina, USA) and sequenced at 100x coverage and 2 x 150 bp read length using the NextSeq 2000 (Illumina, USA) platform. Raw reads were examined for quality [FastQC 0.12.0 software (Babraham Bioinformatics, UK)], trimmed and assembled with CLC Genomics Workbench 24.0.1 (Bio-Qiagen, USA) and SPAdes 3.15.4 (Prjibelski et al., 2020). Annotation was performed using the Jekesa pipeline (Kwenda et al., 2020). Species confirmation and characterisation of AMR, virulence, plasmids, mobile genetic elements (MGEs) and genotyping were conducted using the following Centre for Genomic Epidemiology tools: SpeciesFinder (Larsen et al., 2014), ResFinder 4.6.0 (Bortolaia et al., 2020), VirulenceFinder 2.0 (Joensen et al., 2014), MGEFinder (Johansson et al., 2020), PlasmidFinder 2.1 (Carattoli et al., 2014), MLST 2.0 (Larsen et al., 2012), spaTyper (Bartels et al., 2014) and SCC mec Finder 1.2 (Kaya et al., 2018). Supplementary databases used included the Comprehensive Antibiotic Resistance Database (Alcock et al., 2023) and the Virulence Factor Database (Liu et al., 2022). Pairwise nucleotide polymorphism (SNP) differences were determined using the Split Kmer Analysis toolkit (Liu et al., 2022). Statistical analysis Continuous variables were summarised as means (range) and medians [interquartile range (IQR)], while categorical data were reported as frequencies, proportions and 95% confidence intervals (CIs). Group comparisons were performed using Fisher’s exact test for categorical data and the Mann-Whitney U test for continuous variables, where data did not meet the assumptions of normality. Correlations were assessed using point biserial (rpb) and Kendal tau-b (τb) non-parametric tests to explore relationships between infection type (SAB and SAIE) and continuous (biofilm OD) or categorical variables (sex, ward group and risk factors). A binary logistic regression model was used to identify independent predictors of SAIE, evaluating associations with clinical characteristics including intravenous drug use (IVDU), human immunodeficiency virus (HIV) status and hepatitis C co-infection. Statistical analyses were performed using STATA 16.0 (StataCorp, USA), with two-tailed P < 0.05 considered statistically significant and P < 0.01 or P < 0.001 interpreted as indicating stronger evidence against the null hypothesis. RESULTS Demographical and clinical characteristics The majority [70.1% (54/77)] of the S. aureus isolates were SAB, while SAIE accounted for 29.9% (23/77) of the study isolates. The patient demographic and clinical characteristics are presented in Table 1. Isolates with incomplete data for specific variables were excluded from relevant analyses, resulting in data point variability. A significant association was found between infection type and sex (P < 0.001), with SAIE occurring predominantly among male patients [95.7% (22/23)]. The age of SAIE patients ranged from 22 to 45 years [median = 33, IQR = 30-36], while SAB patients ranged from 4 days to 76 years (median = 32, IQR = 23.5-41). Table 2 summarises the logistic regression results for predictors of SAIE. The model was statistically significant (χ² = 14.54, P < 0.01) and explained 26.2% of the variance in infection type. Recreational IVDU emerged as a strong predictor of SAIE (odds ratio = 7.46, 95% CI: 1.24–45.05, P < 0.05), which aligned with univariate findings of PWID-SAIE association (τb = 0.55, P < 0.001). No significant associations were observed for HIV or hepatitis C after adjusting for IVDU. [Insert Table 1 near here] [Insert Table 2 near here] Antimicrobial resistance profiles All isolates, excluding one SAB isolate, had phenotypic AST data available. Multidrug resistance, defined as resistance to ≥3 antimicrobial classes (Garrine et al., 2023), was observed in 19.7% (15/76) of the isolates, with a higher rate in SAB [24.5% (13/53)] than SAIE [8.7% (2/23)], though not statistically significant. Molecular screening of the mecA gene showed that 13% [10/77 (9 SAB, 1 SAIE)] of isolates were MRSA, largely consistent with AST, except for two phenotypic MRSA isolates lacking mecA and one mecA -positive isolate appearing susceptible. While overall resistance to gentamicin and clindamycin was low, significantly higher rates were observed in the SAB group [18.9% (10/53) and 20.8% (11/53), respectively] compared to the SAIE group (0%; P < 0.05). Inducible clindamycin resistance (ICR) was detected exclusively in SAB isolates [11.3% (6/53)], indicative of an inducible macrolides, lincosamides and streptogramin B (MLSB) resistance phenotype. Benzylpenicillin [79.0% (60/76)] and trimethoprim/sulfamethoxazole [TMP/SMX; 51.3% (39/76)] resistance were most frequent, while resistance to the remaining antimicrobials ranged from 1.3% (1/76) to 17.1% (13/76) and are detailed in Fig. 1. All isolates were susceptible to ampicillin, cefoxitin, fusidic acid, linezolid, mupirocin, streptomycin, teicoplanin, tigecycline and vancomycin. [Insert Fig. 1 near here] Virulence gene distribution and biofilm-forming capacity All 77 isolates (54 SAB, 23 SAIE) were assessed for virulence-associated traits, including the presence of key virulence genes and biofilm formation. The majority of isolates harboured 10 or more virulence genes [53.7% (29/54) SAB; 60.9% (14/23) SAIE], with Fig. 2 illustrating virulence gene distributions by infection type. All isolates harboured icaA and isdB, with frequent co-occurrence of sspB and/or scpA observed in 88.9% (48/54) of SAB and 91.3% (21/23) of SAIE isolates. Adhesion gene combinations involving fnbpA and isdB were common, with fnbpA and isdB present in 79.6% (43/54) of SAB and 78.3% (18/23) of SAIE, while clfA , fnbpA and isdB were present in 75.9% (41/54) of SAB and 60.9% (14/23) of SAIE. Most isolates [77.8% (42/54) SAB; 73.9% (17/23) SAIE] harboured all three exoenzyme genes ( scpA , sspB , vWbp ), while most carried no PTSAg genes [68.5% (37/54) SAB; 69.6% (16/23) SAIE]. The majority of SAB [44.4% (24 /54)] and SAIE [39.1% (9/23)] isolates harboured neither of the two cytolytic toxins ( pvl and hlb ). The most common toxin gene combinations present were as follows: i) hlb and pvl [27.8% (15/54) SAB; 34.8% (8/23) SAIE] and ii) the egc encompassing seg , sei , sem , sen , seo and sometimes sel-u [22.2% (12/54) SAB; 26.1% (6/23) SAIE]. No significant difference was observed in the overall possession of individual virulence genes (P > 0.05) or mean number of virulence genes per isolate (mean = 10, SD = 3.6-3.9, P > 0.05). Overall, 89.6% (69/77) of isolates demonstrated biofilm-forming capacity (Table 3). While strong biofilm formation was more frequent in SAIE [52.2% (12/23)] than SAB [33.3% (18/54)], the overall association between infection type and biofilm category was not significant (P > 0.05). [Insert Fig. 2 near here] [Insert Table 3 near here] Phylogenetic clustering Three major pulsotypes, 15 minor pulsotypes, 26 singletons and two untypable SAB isolates were identified (Fig. 3). Significant associations were found between specific pulsotypes and several genes [ mecA, cna, eap, egc, hlb, pvl , sdre (P ≤ 0.001)], as well as between pulsotypes and AMR [ciprofloxacin, clindamycin, erythromycin, gentamicin, oxacillin, tetracycline, TMP/SMX (P < 0.05); moxifloxacin (P < 0.01)]. Notably, pulsotypes K and O, both mecA -positive, demonstrated resistance to all of the above-mentioned antimicrobials, except TMP/SMX, while pulsotypes E, H–J and P were exclusively pvl -positive. [Insert Fig. 3 near here] Genomic characteristics of representative isolates The 12 representative S. aureus isolates revealed diverse genomic characteristics. Four isolates (SA51, SA53, SA5A and SA12A) demonstrated high genetic similarity, with a mean SNP value of 151 (116 to 175). The genomic similarity between the 12 representative isolates, generated using Proksee (Grant et al., 2023), is shown in Fig. 4. Isolate typing revealed 11 distinct staphylococcal protein A ( spa ) types and eight different sequence types (STs) across seven clonal complexes (CCs). The most common spa type was t355 [16.7% (2/12); both SAIE], while ST152 was predominant [33.3% (4/12); 1 SAB, 3 SAIE]. Among all representative isolates, 58.3% (7/12) belonged to just two CCs (CC152 and CC8). Two MRSA SAB isolates carried staphylococcal cassette chromosome methicillin (SCC mec ) types III (3A) and IVd (2B), while all isolates harboured at least one plasmid, with 83.3% (10/12) carrying multiple plasmid replication protein (Rep) genes ( rep ). The most common plasmid types were Inc18/Rep3, with rep 5a_1 and rep 16_3 present in 58.3% [7/12 (2 SAB, 5 SAIE)] of isolates. Insertion sequences (IS) were identified in 58.3% [7/12 (5 SAB, 2 SAIE)] of isolates, with IS Sau3 most prevalent in 25% [3/12 (1 SAB, 2 SAIE)]. In contrast, composite transposons (CNs), specifically CN_2257_IS Sau6 and CN_12274_IS Sau6 , were only harboured by one SAB isolate. Table S2 (Online Resource 1) summarises the overall WGS results, including STs, CCs, mobilome, resistome and virulome identified in the representative SAB and SAIE isolates, while Table S3 (Online Resource 1) indicates the strain typing results of individual representative isolates. The most prevalent AMR genes and mechanisms identified included: the multidrug efflux transporter ( mepA ) and tetracycline efflux major facilitator superfamily (MFS) transporter [ tet (38)] present in 100% of the isolates, followed by penicillin-hydrolysing class A β-lactamase ( blaZ ) and penicillinase repressor ( blaI ) in 91.7% [11/12 (5 SAB, 6 SAIE)]. The gentamicin resistance aac (6') -Ie/aph (2'') -Ia gene, as well as the MLSB cross-resistance genes erm (ACT), were observed exclusively in SAB isolates [50% (3/6)]. Biocide and heavy metal stress response genes observed included: the multidrug efflux MFS transporter ( lmrS ), linked to resistance against macrolides and phenicols, which was present in 100% of the isolates, followed by cadmium resistance transporter D ( cadD ), present in 91.7% [11/12 (5 SAB, 6 SAIE)]. Adhesion genes, crucial for colonisation and biofilm formation, were widely detected with the autolysin ( atl ), elastin binding protein ( ebp ), fnbpA , icaACR , and spa genes present in 100% of isolates. Enzymatic virulence genes were extensively represented with 100% of isolates harbouring glycerol ester hydrolase ( geh ), hyaluronate lyase ( hysA ), lipase ( lip ), nuc , serine V8 protease ( sspABC ), Coa ( coa ) gene and zinc metalloproteinase aureolysin ( aur ). The toxin virulence gene profiles, including enterotoxins, exfoliative toxins, exotoxins, haemolysins and leukocidins, revealed diverse representation across isolates. The alpha-haemolysin ( hly / hla ), delta haemolysin ( hld ), and bi-component gamma-haemolysin (Hlg) subunits A and B [ hlg ( hlgA and hlgB )] genes were present in 100% of the isolates, while the PVL bi-component subunit F and S [ lukFS-PV (1 SAB, 3 SAIE)] were present in 33.3% (4/12) of the isolates. All isolates harboured the type VII secretion system (T7SS) accessory factor A gene ( esaAG ), essABC and esxA . The WGS AMR and virulence profiles of each representative SAB and SAIE isolate are illustrated in Fig. 5. DISCUSSION Infective endocarditis is considered a rare manifestation of SAB; however, 29.9% of SAB cases in this study were linked to SAIE, exceeding global estimates ranging from as low as 6% in Asia to around 15% in SA and up to 27% in Switzerland (John et al., 2024 ; Ngiam et al., 2024 ; Papadimitriou-Olivgeris et al., 2024 ). Public hospitals in Gauteng, serving around 77.6% of the province’s population, predominantly care for socioeconomically disadvantaged patients with higher rates of immunodeficiency, comorbidities and IVDU, factors that may have contributed to the observed overrepresentation of SAIE (Stats SA, 2023 ). The data suggested demographic disparities, with SAIE cases showing a higher male predominance (95.7%) compared to the 60–70% typically reported in LMICs and HICs (Ahtela et al., 2021 ; Pecoraro et al., 2021 ). Additionally, both SAB and SAIE mainly affected younger adults (25–44 years), aligning with SA data (Pecoraro et al., 2021 ; John et al., 2024 ), but contrasting with HICs, where cases mainly occur in those over 60 years (Ahtela et al., 2021 ; Papadimitriou-Olivgeris et al., 2024 ). These patterns likely reflect the influence of socioeconomic and healthcare challenges in SA [poverty, limited healthcare access, HIV, tuberculosis (TB), prior rheumatic heart disease and IVDU] that often disproportionately affect males in LMICs and drive earlier disease onset (de Villiers, 2021 ; Pecoraro et al., 2021 ). In contrast, HICs trends are shaped by ageing populations with higher burdens of degenerative valvular disease and HA risk (Cahill et al., 2017 ), while oestrogen’s reported cardioprotective effects may partly explain the low representation of female SAIE cases observed (Dohmen et al., 2016 ). The strong SAIE–PWID association observed reflects how non-sterile injection practices introduce pathogens and endocardial-damaging particles, while illicit drug-induced immunosuppression further exacerbates PWID health risks (Masters et al., 2025 ). However, this study’s high prevalence of PWIDs (29.5%), over three times that of a 2024 SA study (9.5%) (John et al., 2024 ), combined with multiple comorbidities and co-infections, highlights the substantial health burden in this vulnerable population. The distribution of S. aureus isolates across hospitals and wards highlighted potential epidemiological and HA patterns. Nearly half (49.4%) of the S. aureus isolates were likely community-associated (CA), inferred from the high proportion originating from emergency wards. Speculatively, the concentration of SAIE and PWID cases in the emergency ward (P < 0.001) may reflect delayed care-seeking among PWIDs due to stigma, limited healthcare access or concerns about legal and social repercussions (Masters et al., 2025 ). Conversely, SAB occurred significantly more often in high-dependency wards (P < 0.05), consistent with the elevated infection risk associated with critical illness, invasive procedures and extended hospitalisation (Samuel et al., 2023 ). Multidrug resistance remains an ever-present challenge in managing bacterial infections, with SAB MDR rates from this study comparable to that of a 2023 study from another LMIC, Mozambique (25%) (Garrine et al., 2023 ). While the study’s SAB (16.7%) MRSA prevalence aligned with Africa’s regional mean of 18% (Haindongo et al., 2023 ), the lower SAIE MRSA rate (4.4%) contrasted with higher rates of 25–43% reported in Asia and the USA (Kanyo et al., 2021 ; Ngiam et al., 2024 ). The lower resistance rates observed in SA may be attributed to improved infection control and antimicrobial stewardship initiatives (Segal et al., 2023 ). The TMP/SMX resistance rates (51.3%), well above the 19% reported in a 2017 SA study, may be driven by routine use as a cost-effective first-line agent and HIV-related prophylaxis outlined by SA treatment guidelines (Moodley and Perovic, 2017 ; Takuva and Nabyoma, 2017). Gentamicin, previously part of SAB and SAIE standard treatment recommendations, is now largely avoided due to nephrotoxicity concerns and limited clinical benefit, except in cases of prosthetic valve IE (Habib et al., 2015 ). Conversely, clindamycin remains an alternative for severe staphylococcal infections, particularly in penicillin-allergic patients and for IE prophylaxis during dental procedures (National Department of Health, 2019 ). Given the historical and current use of gentamicin and clindamycin in SA, the absence of resistance in SAIE isolates compared to SAB may reflect their predominantly CA origin and limited prior antimicrobial exposure, unlike the more HA SAB isolates; however, further research is needed to clarify this discrepancy. The detection of ICR exclusively among SAB isolates highlights the need for routine testing, as undetected inducible MLSB phenotypes may evolve into constitutive forms under treatment pressure, increasing the risk of therapeutic failure (Memariani et al., 2021 ). While few studies have examined the AMR profiles of SAIE isolates, in this study, resistance among SAIE was generally lower than previously reported in another LMIC (Gupta et al., 2021 ). The lower overall resistance rates observed in SAIE isolates might reflect the metabolic costs of maintaining broad-spectrum AMR mechanisms. In the transition from SAB to SAIE, it is plausible that S. aureus may reduce its resistance burden to optimise virulence fitness and the ability to invade and persist in the more stringent endocardial environment (Beceiro et al., 2013 ). Both SAB and SAIE isolates displayed similarly robust virulence potential. The high prevalence of adhesion ( clfA , cna , eap , icaA , isdB and fnbpA) and exoenzyme-associated ( scpA , sspB and vWbp ) genes was expected, given their importance in promoting bacterial adhesion, immune evasion, nutrient acquisition and biofilm modulation in invasive S. aureus infections (Kinney et al., 2022a ; Kinney et al., 2022b ). Although both infection types showed a high capacity for strong biofilm formation, SAIE isolates more often produced particularly robust biofilms. However, despite links to invasive disease severity and endocardial persistence, the lack of correlation between biofilm strength and infection type supports evidence that biofilm formation alone cannot predict IE development, serving as just one of many factors influencing infection outcomes (Bouchiat et al., 2015 ). The lack of significant differences in virulence gene distributions or biofilm formation suggests that the ability to cause severe invasive disease may be an inherent trait of most S. aureus strains. Consistent with this study’s findings, Tristan et al. ( 2012 ) found no distinct virulence genotypes distinguishing SAIE from SAB, while Bastien et al. ( 2023 ) reported no differences in adhesion or IE propensity in murine and mechanical models. These observations suggest that specific virulence factors are unlikely to serve as reliable markers for SAIE risk. If specific determinants of SAIE development risk do exist, they are unlikely to be driven by a single genomic trait; rather, more likely arising from the interplay of multiple biological processes that converge on a shared phenotype - an increased propensity to cause SAIE. Thus, environmental, genetic and host-related risk factors (comorbidities, immune status and at-risk behaviour) may ultimately play a greater role in driving disease progression. Genotyping revealed considerable genetic diversity across both SAB and SAIE isolates, with no clear pulsotype-based distinction, indicating infections arose from diverse backgrounds rather than a single clonal lineage, as supported by WGS and consistent with previous studies (Bouchiat et al., 2015 ; Lilje et al., 2017 ). The identification of closely related isolates among PWIDs raised concerns about potential outbreak risks in this vulnerable group, linked to the circulating endemic PVL-positive ST152/CC152 lineage, previously implicated in outbreaks among SA gold miners in 2017 (Ismail et al., 2020 ). The major African MSSA ST152 clone, which was prevalent among SAIE isolates in this study, is associated with invasive infections and increased SAIE severity, likely driven by its consistent PVL-positive nature, a trait absent from other STs in this study (Lawal et al., 2022 ). In contrast, the pandemic CC8 was exclusively associated with SAB isolates, including well-known HA-MRSA clones such as ST239, ST508 and ST612 (Singh-Moodley et al., 2020 ; Lawal et al., 2022 ; Hetsa et al., 2024 ). Interestingly, CCs traditionally linked to SAIE, including CC5, CC8, CC15 and CC45, were only detected among SAB isolates (Tristan et al., 2012 ; Bouchiat et al., 2015 ). This variation may have reflected regional differences in clonal distribution or suggested that SAIE isolates in SA belong to a broader range of CCs than elsewhere (Lawal et al., 2022 ; Hetsa et al., 2024 ). The presence of genetically related isolates from both SAB and SAIE cases (SA5A and SA51, both ST152-t355) suggests that all SAB isolates, regardless of genotype, may have the potential to cause SAIE under opportunistic conditions. However, further epidemiological studies with larger WGS sample sizes are needed to confirm the associations in SA clinical settings. Representative SAB isolates harboured a wider variety of MGEs, likely influenced by their HA origin, where MGE acquisition is common (Samuel et al., 2023 ). The detection of SCC mec types III (3A) and IVd (2B) aligned with regional data as dominant SCC mec types (Singh-Moodley et al., 2020 ). Specifically, the Brazilian/Hungarian clone t037-ST239-MRSA-III (CC8) and ST612-MRSA-IV clone (CC8) continued to circulate within the study setting, reflecting the endemic status (Singh-Moodley et al., 2020 ). Whole-genome sequencing provided a detailed analysis of AMR genes present, which aligned with phenotypic AST results. The erm genes associated with clindamycin and MLSB resistance were often found on MGEs, while erm (AC) genes in the representative isolates were occasionally chromosomally encoded, likely explaining the variable clindamycin resistance observed among SAB isolates (Memariani et al., 2021 ). Contrary to the low toxin presence in the M-PCR assay results, exotoxins and haemolysins were more dominant in the subset of WGS isolates. Fully functional leukocidins, including the complete bicomponent PVL ( lukFS-PV ) in 33.33% (4/12) of isolates and leukocidin ED ( lukED ) in 41.67% (5/12) of isolates, were observed. The HlgAB subunits were present in all isolates, while only 67% (8/12) of isolates carried the hlgC gene necessary for HlgCB activity. The findings indicated variability in leukocidin composition and suggested potential diverse functional capabilities among the representative S. aureus isolates. The universal presence of the icaAC genes, along with the high prevalence of the icaB gene [91.7% (11/12)], suggested a robust capacity for biofilm initiation and maturation during invasive infections (Peng et al., 2022 ). While present in both groups, nearly all SAIE isolates (excluding one) harboured the complete set of 12 T7SS genes, compared to the more variable presence in SAB. This complete T7SS repertoire in SAIE suggests enhanced colonisation, immune evasion and interbacterial competition with T7SS gene content variation likely influenced by host-derived signals that modulate T7SS activation, which may differ between cardiac tissue and bloodstream environments (Boardman et al., 2023 ). This study provides a comprehensive comparison of the phenotypic, genotypic and patient characteristics of SAB and SAIE isolates within a SA context. However, the observational retrospective nature of this study posed inherent challenges. The modest sample size and uneven distribution of infection types likely reduced statistical power to detect smaller effects, while limited or absent clinical information introduced a potential risk of infection type misclassification. Nonetheless, these limitations reflect the real-world data collection constraints typical of LMIC public health sector research. Future studies should explore the relationship between patient characteristics, S. aureus infection dynamics and the SAB to SAIE progression in LMICs. Continued surveillance is essential to monitor and address the unique challenges posed by S. aureus infections in LMICs. CONCLUSION The study provided valuable insights into the AMR and pathogenic profiles of invasive S. aureus isolates from public healthcare settings in Gauteng, SA. No distinct phenotypic or genetic markers were explicitly linked to SAIE compared to SAB isolates, except for gentamicin and clindamycin resistance exclusive to SAB isolates, suggesting that all SAB isolates may possess the pathogenic potential to progress to IE. Additionally, while pathogenic traits of S. aureus are important, host factors, particularly among high-risk groups, may play a more pivotal role in predicting disease progression. The high prevalence of PWID-associated SAIE observed underscores the need for targeted public health interventions and holistic strategies to address modifiable risk factors in both SAB and SAIE management. Declarations Acknowledgements The authors would like to acknowledge the National Health Laboratory Service (NHLS) for funding this study. Ms Spaltman would like to acknowledge the National Research Foundation (NRF) and the Oppenheimer Memorial Trust (OMT) for their financial support. The views expressed in this study and the conclusions formulated are the authors’ and are not to be attributed to those of the NHLS, NRF or OMT. Funding This study was supported by the National Health Laboratory Service (NHLS). Declaration of competing interests The authors declare no competing interests. Author Contributions LDS: Conceptualisation and study design; investigation; methodology; data curation; formal analysis; writing - original draft preparation; writing - review and editing. TH: Conceptualisation and study design; supervision; writing - review and editing. VU: Assistance with retrospective clinical data acquisition; writing - review and editing. MK: Technical assistance with dendrogram construction; writing - review and editing. AB: Assistance with initial patient data collection and isolate procurement; supervision; writing - review and editing. MME: Conceptualisation and study design; supervision; resources; funding acquisition; writing - review and editing. All authors contributed to the article and approved the submitted version. Data availability The whole-genome sequencing datasets generated and analysed during this study have been deposited in the DDBJ/ENA/GenBank under BioProject number PRJNA1366126, with accession numbers SAMN53307515-SAMN53307526. All other datasets used and analysed during the current study are available from the corresponding author on reasonable request. Ethics declarations Ethics approval and consent to participate This study was performed in accordance with the principles of the Declaration of Helsinki. Ethical approval was granted by the University of Pretoria, Faculty of Health Sciences Research Ethics Committee (Reference number: 183/2023). Informed consent was waived due to the retrospective nature of the study, with all patient information de-identified and anonymised prior to analysis. References Achoki T, Sartorius B, Watkins D, Glenn SD, Kengne AP, Oni T, Wiysonge CS, Walker A, Adetokunboh OO, Babalola TK, Bolarinwa OA, Claassens MM, Cowden RG, Day CT, Ezekannagha O, Ginindza TG, Iwu CCD, Iwu CJ, Karangwa I, Katoto PD, Kugbey N, Kuupiel D, Mahasha PW, Mashamba-Thompson TP, Mensah GA, Ndwandwe DE, Nnaji CA, Ntsekhe M, Nyirenda TE, Odhiambo JN, Oppong Asante K, Parry CDH, Pillay JD, Schutte AE, Seedat S, Sliwa K, Stein DJ, Tanser FC, Useh U, Zar HJ, Zühlke LJ, Mayosi BM, Hay SI, Murray CJL, Naghavi M (2022) Health trends, inequalities and opportunities in South Africa's provinces, 1990-2019: Findings from the Global Burden of Disease 2019 study. J Epidemiol Community Health 76:471–81. https://doi.org/10.1136/jech-2021-217480. Agnello S, Wardlow LC, Reed E, Smith JM, Coe K, Day SR (2021) Clinical outcomes of daptomycin versus anti-staphylococcal beta-lactams in definitive treatment of methicillin-susceptible Staphylococcus aureus bloodstream infections. Int J Antimicrob Agents 58:106363. https://doi.org/10.1016/j.ijantimicag.2021.106363. Ahtela E, Oksi J, Vahlberg T, Sipilä J, Rautava P, Kytö V (2021) Short- and long-term outcomes of infective endocarditis admission in adults: A population-based registry study in Finland. PLoS ONE 16:e0254553. https://doi.org/10.1371/journal.pone.0254553. Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR, Wlodarski MA, Edalatmand A, Petkau A, Syed SA, Tsang KK, Baker SJC, Dave M, McCarthy MC, Mukiri KM, Nasir JA, Golbon B, Imtiaz H, Jiang X, Kaur K, Kwong M, Liang ZC, Niu KC, Shan P, Yang JYJ, Gray KL, Hoad GR, Jia B, Bhando T, Carfrae LA, Farha MA, French S, Gordzevich R, Rachwalski K, Tu MM, Bordeleau E, Dooley D, Griffiths E, Zubyk HL, Brown ED, Maguire F, Beiko RG, Hsiao WWL, Brinkman FSL, Van Domselaar G, McArthur AG (2023) CARD 2023: Expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res 51:D690–d699. https://doi.org/10.1093/nar/gkac920. Barbosa C, Nogueira S, Gadanho M, Chaves S (2016) DNA extraction: Finding the most suitable method. In: Cook N, D'Agostino M, Thompson KC (ed). Molecular microbial diagnostic methods 2016:135–154. https:/doi.org/10.1016/B978-0-12-416999-9.00007-1. Bartels MD, Petersen A, Worning P, Nielsen JB, Larner-Svensson H, Johansen HK, Andersen LP, Jarløv JO, Boye K, Larsen AR, Westh H (2014) Comparing whole-genome sequencing with Sanger sequencing for spa typing of methicillin-resistant Staphylococcus aureus . J Clin Microbiol 52:4305–8. https://doi.org/10.1128/jcm.01979-14. Bastien S, Meyers S, Salgado-Pabón W, Giulieri SG, Rasigade J-P, Liesenborghs L, Kinney KJ, Couzon F, Martins-Simoes P, Moing VL, Duval X, Holmes NE, Bruun NE, Skov R, Howden BP, Fowler VG, Verhamme P, Andersen PS, Bouchiat C, Moreau K, Vandenesch F (2023) All Staphylococcus aureus bacteraemia-inducing strains can cause infective endocarditis: Results of GWAS and experimental animal studies. J Infect 86:123–133. https://doi.org/10.1016/j.jinf.2022.12.028. Beceiro A, Tomás M, Bou G (2013) Antimicrobial resistance and virulence: A successful or deleterious association in the bacterial world? Clin Microbiol Rev 26:185–230. https://doi.org/10.1128/cmr.00059-12. Boardman ER, Palmer T, Alcock F (2023) Interbacterial competition mediated by the type VIIb secretion system. Microbiology (Reading) 169. https://doi.org/10.1099/mic.0.001420. Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nykäsenoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75:3491–3500. https://doi.org/10.1093/jac/dkaa345. Bouchiat C, Moreau K, Devillard S, Rasigade J-P, Mosnier A, Geissmann T, Bes M, Tristan A, Lina G, Laurent F, Piroth L, Aissa N, Duval X, Le Moing V, Vandenesch F, Chirouze C, Curlier E, Descottes-Genon C, Hoen B, Patry I, Vettoretti L, Chavanet P, Eicher J-C, Gohier-Treuvelot S, Greusard M-C, Neuwirth C, Péchinot A, Piroth L, Célard M, Cornu C, Delahaye F, Hadid M, Rausch P, Coma A, Galtier F, Géraud P, Jean-Pierre H, Le Moing V, Sportouch C, Reynes J, Aissa N, Doco-Lecompte T, Goehringer F, Keil N, Letranchant L, Malela H, May T, Selton-Suty C, Bedos N, Lavigne J-P, Lechiche C, Sotto A, Duval X, Habensus EI, Iung B, Leport C, Longuet P, Ruimy R, Bellissant E, Donnio P-Y, Le Gac F, Michelet C, Revest M, Tattevin P, Thebault E, Alla F, Braquet P, Erpelding M-L, Minary L, Tubiana S, Bès M, Etienne J, Tristan A, Vandenesch F, Barbas S, Delonca C, Sussmuth V, Verchère A (2015) Staphylococcus aureus infective endocarditis versus bacteremia strains: Subtle genetic differences at stake. Infect Genet Evol 36:524–530. https://doi.org/10.1016/j.meegid.2015.08.029. Cahill TJ, Baddour LM, Habib G, Hoen B, Salaun E, Pettersson GB, Schäfers HJ, Prendergast BD (2017) Challenges in infective endocarditis. J Am Coll Cardiol 69:325–344. https://doi.org/10.1016/j.jacc.2016.10.066. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H (2014) in silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895–903. https://doi.org/10.1128/aac.02412-14. de Villiers K (2021) Bridging the health inequality gap: An examination of South Africa’s social innovation in health landscape. Infect Dis Poverty 10:19. https://doi.org/10.1186/s40249-021-00804-9. Dohmen PM, Binner C, Mende M, Daviewala P, Etz CD, Borger MA, Misfeld M, Eifert S, Mohr FW (2016) Gender-based long-term surgical outcome in patients with active infective aortic valve endocarditis. Med Sci Monit 22:2520–2527. https://doi.org/10.12659/msm.899360. Garrine M, Costa SS, Messa A, Jr., Massora S, Vubil D, Ácacio S, Nhampossa T, Bassat Q, Mandomando I, Couto I (2023) Antimicrobial resistance and clonality of Staphylococcus aureus causing bacteraemia in children admitted to the Manhiça District Hospital, Mozambique, over two decades. Front Microbiol 14:1208131. https://doi.org/10.3389/fmicb.2023.1208131. Grant JR, Enns E, Marinier E, Mandal A, Herman EK, Chen C-y, Graham M, Van Domselaar G, Stothard P (2023) Proksee: In-depth characterization and visualization of bacterial genomes. Nucleic Acids Res 51:W484–W492. https://doi.org/10.1093/nar/gkad326. Gupta R, Kaushal V, Goyal A, Kumar P, Gupta D, Tandon R, Mahajan A, Singla S, Singh G, Singh B, Chhabra ST, Aslam N, Wander GS, Gupta V, Mohan B (2021) Changing microbiological profile and antimicrobial susceptibility of the isolates obtained from patients with infective endocarditis – The time to relook into the therapeutic guidelines. Indian Heart J 73:704–710. https://doi.org/10.1016/j.ihj.2021.10.013. Habib G, Lancellotti P, Antunes MJ, Bongiorni MG, Casalta J-P, Del Zotti F, Dulgheru R, El Khoury G, Erba PA, Iung B, Miro JM, Mulder BJ, Plonska-Gosciniak E, Price S, Roos-Hesselink J, Snygg-Martin U, Thuny F, Tornos Mas P, Vilacosta I, Zamorano JL, Group ESD (2015) 2015 ESC Guidelines for the management of infective endocarditis: The task force for the management of infective endocarditis of the European Society of Cardiology (ESC)Endorsed by: European Association for Cardio-Thoracic Surgery (EACTS), the European Association of Nuclear Medicine (EANM). Eur Heart J 36:3075–3128. https://doi.org/10.1093/eurheartj/ehv319. Haindongo EH, Ndakolo D, Hedimbi M, Vainio O, Hakanen A, Vuopio J (2023) Antimicrobial resistance prevalence of Escherichia coli and Staphylococcus aureus amongst bacteremic patients in Africa: A systematic review. J Glob Antimicrob Resist 32:35–43. https://doi.org/10.1016/j.jgar.2022.11.016. Hetsa BA, Asante J, Mbanga J, Ismail A, Abia ALK, Amoako DG, Essack SY (2024) Genomic characterization of methicillin-resistant and methicillin-susceptible Staphylococcus aureus implicated in bloodstream infections, KwaZulu-Natal, South Africa: A pilot study. Antibiotics 13:796. https://doi.org/10.3390/antibiotics13090796. Ismail H, Govender NP, Singh-Moodley A, van Schalkwyk E, Shuping L, Moema I, Feller G, Mogokotleng R, Strasheim W, Lowe M, Mpembe R, Naicker S, Maphanga TG, De Abreu C, Ismail F, Ismail N, Allam M, Ismail A, Singh T, Matuka O, Duba T, Perovic O (2020) An outbreak of cutaneous abscesses caused by Panton-Valentine leukocidin-producing methicillin-susceptible Staphylococcus aureus among gold mine workers, South Africa, November 2017 to March 2018. BMC Infect Dis 20:621. https://doi.org/10.1186/s12879-020-05352-5. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM (2014) Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli . J Clin Microbiol 52:1501–10. https://doi.org/10.1128/jcm.03617-13. Johansson MHK, Bortolaia V, Tansirichaiya S, Aarestrup FM, Roberts AP, Petersen TN (2020) Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J Antimicrob Chemother 76:101–109. https://doi.org/10.1093/jac/dkaa390. John M, Richards L, Nel JS (2024) Staphylococcus aureus bacteraemia cases at Helen Joseph Hospital. S Afr J Infect Dis 39. https://doi.org/10.4102/sajid.v39i1.626. Kanyo EC, Nowacki AS, Gordon SM, Shrestha NK (2021) Comparison of mortality, stroke, and relapse for methicillin-resistant versus methicillin-susceptible Staphylococcus aureus infective endocarditis: A retrospective cohort study. Diagn Microbiol Infect Dis 100:115395. https://doi.org/10.1016/j.diagmicrobio.2021.115395. Kaya H, Hasman H, Larsen J, Stegger M, Johannesen TB, Allesøe RL, Lemvigh CK, Aarestrup FM, Lund O, Larsen AR (2018) SCCmecFinder, a web-based tool for typing of staphylococcal cassette chromosome mec in Staphylococcus aureus using whole-genome sequence data. mSphere 3:00612–17. https://doi.org/10.1128/msphere.00612-17. Kinney KJ, Stach JM, Kulhankova K, Brown M, Salgado-Pabón W (2022a) Vegetation formation in Staphylococcus aureus endocarditis inversely correlates with RNAIII and sarA expression in invasive clonal complex 5 isolates. Front Cell Infect Microbiol 12. https://doi.org/10.3389/fcimb.2022.925914. Kinney KJ, Tang SS, Wu X-J, Tran PM, Bharadwaj NS, Gibson-Corley KN, Forsythe AN, Kulhankova K, Gumperz JE, Salgado-Pabón W (2022b) SEC is an antiangiogenic virulence factor that promotes Staphylococcus aureus endocarditis independent of superantigen activity. Sci Adv 8:eabo1072. https://doi.org/10.1126/sciadv.abo1072 Kwenda S, Khumalo Z, Mtshali S, Mnyameni F, Ismail A (2020) Jekesa: An automated easy-to-use pipeline for bacterial whole genome typing, 2020. https://github.com/stanikae/jekesa. Accessed 21 Nov 2024. Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pontén T, Aarestrup FM, Ussery DW, Lund O (2014) Benchmarking of methods for genomic taxonomy. J Clin Microbiol 52:1529–39. https://doi.org/10.1128/jcm.02981-13. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pontén T, Ussery DW, Aarestrup FM, Lund O (2012) Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:1355–61. https://doi.org/10.1128/jcm.06094-11. Lawal OU, Ayobami O, Abouelfetouh A, Mourabit N, Kaba M, Egyir B, Abdulgader SM, Shittu AO (2022) A 6-year update on the diversity of methicillin-resistant Staphylococcus aureus clones in Africa: A systematic review. Front Microbiol 13:860436. https://doi.org/10.3389/fmicb.2022.860436. Lilje B, Rasmussen RV, Dahl A, Stegger M, Skov RL, Fowler VG, Ng KL, Kiil K, Larsen AR, Petersen A, Johansen HK, Schønheyder HC, Arpi M, Rosenvinge FS, Korup E, Høst U, Hassager C, Gill SUA, Hansen TF, Johannesen TB, Smit J, Søgaard P, Skytt Andersen P, Eske-Bruun N (2017) Whole-genome sequencing of bloodstream Staphylococcus aureus isolates does not distinguish bacteraemia from endocarditis. Microb Genom 3. https://doi.org/10.1099/mgen.0.000138. Liu B, Zheng D, Zhou S, Chen L, Yang J (2022) VFDB 2022: A general classification scheme for bacterial virulence factors. Nucleic Acids Res 50:D912–d917. https://doi.org/10.1093/nar/gkab1107. Masters J, Goodman-Meza D, Russell D, Marks L, McCreary E, Jacka B, Seear K, Davis JS, Matthews G, Martinello M, Tong SYC, Dore GJ (2025) Bacterial and fungal infections in persons who inject drugs. Clin Microbiol Rev 0:e00162–23. https://doi.org/10.1128/cmr.00162-23. McDougal LK, Steward CD, Killgore GE, Chaitram JM, McAllister SK, Tenover FC (2003) Pulsed-field gel electrophoresis typing of oxacillin-resistant Staphylococcus aureus isolates from the United States: Establishing a national database. J Clin Microbiol 41:5113–5120. https://doi.org/10.1128/jcm.41.11.5113-5120.2003. Memariani M, Memariani H, Moravvej H (2021) Inducible clindamycin resistance among clinical Staphylococcus aureus strains in Iran: A contemporaneous systematic review and meta-analysis. Gene Rep 23:101104. https://doi.org/10.1016/j.genrep.2021.101104. Merritt JH, Kadouri DE, O'Toole GA (2005) Growing and analyzing static biofilms. Curr Protoc Microbiol 2005:1B.1. https://doi.org/10.1002/9780471729259.mc01b01s00. Moodley A, Perovic O (2017) Characterisation of Staphylococcus aureus bloodstream isolates from Gauteng and Western Cape provinces, South Africa, 2016 and 2017. Public Health Surveill Bull 16:99–107. https://www.nicd.ac.za/wp-content/uploads/2018/09/Characterisation-of-Staphylococcus-aureus-bloodstream-isolates-from-Gauteng-and-Western-Cape-provinces-South-Africa-2016-and-2017.pdf. Accessed 23 Mar 2023. National Department of Health (2019) Essential Drugs Programme: Hospital level (Adults) Standard Treatment Guidelines and Essential Medicines List. In: National Department of Health SA editor. Pretoria, Republic of South Africa; 2019. https://knowledgehub.health.gov.za/system/files/elibdownloads/2023-04/Hospital%2520Level%2520%2528Adult%2529%25202019_v2.0.pdf. Accessed 29 Jan 2023. Ngiam JN, Koh MCY, Archuleta S, Fisher D, Chai LY-A, Sia C-H, Kong WKF, Tambyah PA (2024) Performance of risk scores in predicting infective endocarditis in patients with Staphylococcus aureus bacteraemia in a prospective asian cohort. J Clin Med 13:2947. https://doi.org/10.3390/jcm13102947. Papadimitriou-Olivgeris M, Guery B, Monney P, Senn L, Steinmetz S, Boillat-Blanco N (2024) Prevalence of infective endocarditis among patients with Staphylococcus aureus bacteraemia and bone and joint infections. Microorganisms 12:342. https://doi.org/10.3390/microorganisms12020342. Pecoraro AJK, Pienaar C, Herbst PG, Poerstamper S, Joubert L, Taljaard J, Prozesky H, Janson J, Newton-Foot M, Doubell AF (2021) Causes of infective endocarditis in the Western Cape, South Africa: A prospective cohort study using a set protocol for organism detection and central decision making by an endocarditis team. BMJ Open 11:e053169. https://doi.org/10.1136/bmjopen-2021-053169. Peng Q, Tang X, Dong W, Sun N, Yuan W (2022) A review of biofilm formation of Staphylococcus aureus and its regulation mechanism. Antibiotics (Basel) 12. https://doi.org/10.3390/antibiotics12010012. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A (2020) Using SPAdes de novo assembler. Curr Protoc Bioinformatics 70:e102. https://doi.org/10.1002/cpbi.102. Salgado-Pabón W, Breshears L, Spaulding AR, Merriman JA, Stach CS, Horswill AR, Peterson ML, Schlievert PM (2013) Superantigens are critical for Staphylococcus aureus infective endocarditis, sepsis, and acute kidney injury. mBio 4. https://doi.org/10.1128/mBio.00494-13. Samuel P, Kumar YS, Suthakar BJ, Karawita J, Sunil Kumar D, Vedha V, Shah H, Thakkar K (2023) Methicillin-resistant Staphylococcus aureus colonization in intensive care and burn units: A narrative review. Cureus 15:e47139. https://doi.org/10.7759/cureus.47139. Segal B, Langham A, Klevansky R, Patel N, Mokoena T, Nassiep M, Ramatlo O, Ahmad A, Duse AG (2023) Analysis of the trends of methicillin-resistant Staphylococcus aureus in Gauteng public hospitals from 2009 to 2018. Microbiol Spectr 11:e03623–22. https://doi.org/10.1128/spectrum.03623-22. Singh-Moodley A, Lowe M, Mogokotleng R, Perovic O (2020) Diversity of SCCmec elements and spa types in South African Staphylococcus aureus mecA-positive blood culture isolates. BMC Infect Dis 20:816. https://doi.org/10.1186/s12879-020-05547-w. Stats SA (2023) General Household Survey of 2023: Statistical Release. In: Africa DoSS editor. Department of Statistics, Republic of South Africa. Statistical Release. Pretoria: Stats SA; 2023. vol. 318. https://www.statssa.gov.za/publications/P0318/P03182023.pdf. Accessed 11 Nov 2024. Takuva SNabyoma N (2017) South African National essential medicine list adult hospital level medication review process component: HIV and AIDs. In: Health SANDo editor: South African National Department of Health; 2017. https://knowledgehub.health.gov.za/system/files/elibdownloads/2020-07/CD4%20cut-off%20for%20cotrimoxazole%20for%20OI%20prophylaxis%20in%20PLHIV_Adult%20review_16May2017.pdf. Accessed 26 Jun 2023. Tristan A, Rasigade JP, Ruizendaal E, Laurent F, Bes M, Meugnier H, Lina G, Etienne J, Celard M, Tattevin P, Monecke S, Le Moing V, Vandenesch F (2012) Rise of CC398 lineage of Staphylococcus aureus among infective endocarditis isolates revealed by two consecutive population-based studies in France. PLoS ONE 7:e51172. https://doi.org/10.1371/journal.pone.0051172. Tables Table 1: Demographical characteristics of Staphylococcus aureus bacteraemia and infective endocarditis isolate groups Characteristic No. of Isolates with the Characteristic [n=77 (%)] No. of Isolates with the Characteristic by Infection Type Overall P Value Bacteraemia [n=54 (%)] Infective Endocarditis [n= 23 (%)] Subgroup P Value Overall Group P Value Sex a Male 52 (69.33) 30 (57.69) 22 (95.65) 0.001* Female 23 (30.67) 22 (42.31) 1 (4.35) Unknown 2 2 0 N/A Age Groups a <5 years 7 (10.14) 7 (14.58) 0 0.092 0.049* 5 years - 24 years 7 (10.14) 6 (12.50) 1 (4.76) 0.427 25 years - 44 years 44 (63.77) 25 (52.08) 19 (90.48) 0.002* 45 years - 64 years 8 (11.59) 7 (14.58) 1 (4.76) 0.419 >65 years 3 (4.35) 3 (6.25) 0 0.548 Unknown 8 6 2 N/A Hospital b Hospital 1 25 (32.47) 20 (37.04) 5 (21.74) 0.288 0.001* Hospital 2 13 (16.88) 13 (24.07) 0 0.008* Hospital 3 1 (1.30) 1 (1.85) 0 1.000 Hospital 4 20 (25.97) 7 (12.96) 13 (56.52) 0.000* Hospital 5 8 (10.39) 6 (11.11) 2 (8.70) 1.000 Hospital 6 5 (6.49) 3 (5.56) 2 (8.70) 0.632 Hospital 7 5 (6.49) 4 (7.41) 1 (4.35) 1.000 Wards a Emergency 38 (52.78) 19 (38.78) 19 (82.61) 0.000* 0.004* High dependency 15 (20.83) 14 (28.57) 1 (4.35) 0.028* General 17 (23.61) 14 (28.57) 3 (13.04) 0.234 Outpatient 2 (2.78) 2 (4.08) 0 1.000 Unknown 5 5 0 N/A Risk Factors and Clinical Conditions a c Immunocompromised 24 (46.15) 10 (55.56) 14 (41.18) 0.388 Sepsis d 19 (34.55) 4 (22.22) 15 (40.54) 0.234 Living with HIV 16 (30.77) 9 (50.0) 7 (20.59) 0.056 Persons Who Inject Drugs e 13 (29.55) 10 (62.50) 3 (10.71) 0.001* Hepatitis C 9 (17.31) 7 (38.89) 2 (5.88) 0.005* Pneumonia 8 (15.38) 2 (11.11) 6 (17.65) 0.698 Kidney Injury or Disease 8 (15.38) 2 (11.11) 6 (17.65) 0.698 Renal Failure 5 (9.62) 0 5 (14.71) 0.150 Hypertension 5 (9.62) 1 (5.56) 4 (11.76) 0.648 Nosocomial Infection f 4 (7.55) 0 4 (11.43) 0.287 Abbreviations: NA – Not applicable; HIV – Human immunodeficiency virus P < 0.05 was considered statistically significant * Statistically significant observation a Section had a diverging number of data points due to missing patient information b Hospital bed capacity: Hospital 1 – 845 beds; Hospital 2 – 840 beds; Hospital 3 – 44 beds; Hospital 4 – 857 beds; Hospital 5 – 202 beds; Hospital 6 – 153 beds; Hospital 7 – 325 beds. c Data in this sub-section was available for 52 patients (34 SAB, 18 SAIE) unless stated otherwise; deviations from this baseline are indicated per characteristic. d - f Data was available for d 55 patients (37 SAB, 18 SAIE), e 44 patients (28 SAB, 16 SAIE) and f 53 patients (35 SAB, 18 SAIE) Table 2: Logistic regression analysis of potential predictor variables in Staphylococcus aureus infective endocarditis development Predictor Variable Odds Ratio 95% Confidence Interval P-value Intravenous drug use 7.46 1.24 - 45.05 0.028* HIV status 2.15 0.42 - 10.96 0.357 Hepatitis C 3.60 0.45 - 28.96 0.229 Intercept (Baseline Odds) 0.17 0.05 - 0.50 0.002* Abbreviations: HIV – Human immunodeficiency virus P < 0.05 was considered statistically significant. * Statistically significant observation Table 3: Biofilm formation capabilities of the Staphylococcus aureus bacteraemia and infective endocarditis isolates Biofilm Formation Capability No. of Isolates with the Biofilm Formation Capability [n = 77 (%)] No. of Isolates with the Biofilm Formation Capability by Infection Type [n (%)] P value Infective Endocarditis (n = 23) Bacteraemia (n = 54) Mean OD (Range) n (%) Mean OD (Range) n (%) Non 8 (10.39) 0.12 (0.04 – 0.19) 2 (8.70) 0.19 (0.17 – 0.20) 6 (11.11) 1.000 Weak 19 (24.68) 0.26 (0.22 - 0.31) 5 (21.74) 0.26 (0.21 – 0.31) 14 (25.93) 0.780 Moderate 20 (25.97) 0.36 (0.34 – 0.41) 4 (17.39) 0.41 (0.34 – 0.49) 16 (29.63) 0.395 Strong 30 (38.96) 1.03 (0.52 - 2.40) 12 (52.17) 0.85 (0.53 – 1.36) 18 (33.33) 0.134 Abbreviations: OD – Optical density P < 0.05 was considered statistically significant. Additional Declarations No competing interests reported. Supplementary Files SupplementaryMaterial.docx MultiplexPCRVirulenceIsdBicaAHlbSdrE18121820274754.tif MultiplexPCRVirulenceIsdBicaAHlbSdrE3135374146.tif MultiplexPCRVirulenceIsdBicaAHlbSdrE9192A1a2A56A9A.tif MultiplexPCRVirulenceIsdBicaAHlbSdrE7590.tif MultiplexPCRIDVirulence.tif IDvirulence374145525463.tif IDvirulence191A12A.tif MultiplexPCRVirulenceIsdBSdrEicaAHlb91122242653.tif IDvirulence18121920273134.tif MultiplexPCRVirulenceS.EPISEOSEMSELUPVLSEISEN1812182027.tif MultiplexPCRVirulenceIsdBSdrEicaAHlb5574.tif IDvirulence18121920273135374144.tif MultiplexPCRVirulenceSDREHLBICAAISDBSEGSEIPVLSELUSECTST10A12A.tif MultiplexPCRVirulenceS.EPISEOSEMSELUPVLSEISEN18121820273135.tif MultiplexPCRVirulencesemsenseosspb91122242653IsdBSdrEicaAHlb91122242653.tif MultiplexPCRVirulencesemsenseossbp91122242653fnbp47525458.tif MultiplexPCRVirulenceSSPBSEMSEOSEN138121820273135374143.tif MultiplexPCRVirulenceSSPBSEMSEOSEN2A12A.tif MultiplexPCRVirulenceSSPBSEMSEOSEN313344586985.tif MultiplexPCRVirulenceSSPBSEMSEOSEN6168.tif MultiplexPCRVirulencevwbp6669semsenseossbp86921A2A5A9A.tif MultiplexPCRVirulenceSSPBSEMSEOSEN44525460.tif SingleplexPCRVirulencevwbp44525465.tif MultiplexPCRVirulencetstpvlsecselusegsei911222426531A2A5A9A.tif SingleplexPCRVirulenceclfA1381218202731.tif SingleplexPCRVirulenceCNA77929111422.tif SingleplexPCRVirulenceCNA6376.tif SingleplexPCRVirulenceCNA46525462.tif SingleplexPCRVirulenceCNA1381218202731.tif SingleplexPCRVirulenceCNAEAPVWBP2A12A.tif SingleplexPCRVirulenceEAP1381218202731.tif SingleplexPCRVirulenceEAP77929111422.tif SingleplexPCRVirulenceEAP5866CNA32354145.tif SingleplexPCRVirulenceEAP32353741525457.tif SingleplexPCRVirulenceFNBP58121820273135374146.tif SingleplexPCRVirulenceFNBP47525469.tif SingleplexPCRVirulenceScpA2027313537415254.tif SingleplexPCRVirulenceScpA5569.tif Virulencetstsecseisegfnba1812182027.tif Virulencetstsecseisegfnba3135374147.tif Virulencetstsegsecselu48525466.tif Virulencetstsecseisegfnba48525456.tif Virulencetstsegsecselu8092.tif Virulencetstsegsecselu6779.tif Cite Share Download PDF Status: Under Revision Version 1 posted Editorial decision: Revision requested 04 May, 2026 Reviews received at journal 17 Apr, 2026 Reviews received at journal 16 Apr, 2026 Reviewers agreed at journal 19 Mar, 2026 Reviewers agreed at journal 19 Mar, 2026 Reviewers invited by journal 11 Feb, 2026 Editor assigned by journal 27 Jan, 2026 Submission checks completed at journal 27 Jan, 2026 First submitted to journal 23 Jan, 2026 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8678564","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":590863202,"identity":"0faeea6c-dd92-429f-80d6-d313995bb4e7","order_by":0,"name":"Lz D. 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While often transient, unresolved \u003cem\u003eS. aureus\u003c/em\u003e bacteraemia (SAB) infections can progress to severe complications, including \u003cem\u003eS. aureus\u003c/em\u003e IE (SAIE), a rare yet deadly localised endocardial infection with high rates of recurrence (Kinney et al., \u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e2022a\u003c/span\u003e). The emergence of SAIE has become particularly pronounced in South Africa (SA) and is the leading cause of IE among persons who inject drugs (PWIDs) (Pecoraro et al., \u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). With a high proportion of the SA population at risk due to immunocompromising conditions and limited access to quality healthcare, \u003cem\u003eS. aureus\u003c/em\u003e poses a significant public health concern (Achoki et al., \u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). Despite its clinical significance, the characteristics, outcome-related factors and local epidemiology of SAIE in SA healthcare-associated (HA) settings remain underexplored.\u003c/p\u003e \u003cp\u003eThe pathogenic success of \u003cem\u003eS. aureus\u003c/em\u003e arises from extensive antimicrobial resistance (AMR) mechanisms and virulence factors that facilitate host colonisation, immune evasion and persistence (Kinney et al., \u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e2022a\u003c/span\u003e). Cardiac vegetation formation, pathognomonic of SAIE, is promoted by adhesins and coagulases that trigger platelet activation and aggregation, including clumping factor A (ClfA), fibronectin-binding protein A (FnBPA), iron-regulated surface determinant protein B (IsdB), serine-aspartate repeat-containing protein E (SdrE), extracellular adherence protein (Eap), coagulase (Coa) and von Willebrand factor-binding protein (vWbp) (Kinney et al., \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e2022b\u003c/span\u003e). Whereas exoenzymes, haemolysins and superantigens (SAgs) drive the aggressive nature of SAIE (Kinney et al., \u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e2022a\u003c/span\u003e). Specific toxins, including beta (β)-haemolysin (Hlb), staphylococcal enterotoxin (SE) C (SEC), the enterotoxin gene cluster [\u003cem\u003eegc\u003c/em\u003e; SEI, SEM, SEO, SE-like toxin U (SEl-U)] and toxic shock syndrome toxin-1 (TSST-1) are thought to induce disease by altering endothelial cell activity and promoting vegetation (Kinney et al., \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e2022b\u003c/span\u003e). Additionally, SAgs affect SAIE progression by dysregulating immune responses, causing persistent inflammation and cytotoxicity (Salgado-Pab\u0026oacute;n et al., \u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e2013\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe present study was prompted by conflicting evidence on the distinguishability between SAB and SAIE strains. Earlier studies (Salgado-Pab\u0026oacute;n et al., \u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e2013\u003c/span\u003e; Bouchiat et al., \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2015\u003c/span\u003e) suggested certain bacterial phenotypes might be linked to SAIE, whereas a recent multi-high-income country (HIC) study (Bastien et al., \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2023\u003c/span\u003e) found similar pathogenic potential across all SAB and SAIE strains. However, given the absence of African isolates, limited local genomic surveillance and contextual differences between SA and the HICs assessed, whether local strain characteristics follow these trends remained unclear, warranting region-specific investigation. Therefore, this study aimed to characterise \u003cem\u003eS. aureus\u003c/em\u003e isolates associated with SAB and SAIE cases at Gauteng public hospitals to determine whether clinical SAIE isolates are genomically distinguishable from non-IE SAB isolates or whether specific factors influence the progression to SAIE.\u003c/p\u003e"},{"header":"MATERIALS AND METHODS","content":"\u003cp\u003e\u003cstrong\u003eStudy setting and collection of \u003cem\u003eS. aureus\u003c/em\u003e isolates\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eEthical approval for the study was obtained from the University of Pretoria (UP), Faculty of Health Sciences Research Ethics Committee (Reference number: 183/2023). The study was conducted at the Department of Medical Microbiology, UP, using \u003cem\u003eS. aureus\u003c/em\u003e isolates collected between February and November 2023 from a public diagnostic laboratory in Tshwane, SA.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eThis diagnostic laboratory provides services to public clinics and hospitals at both primary and tertiary levels within the city of Tshwane and surrounding areas. The \u003cem\u003eS. aureus\u0026nbsp;\u003c/em\u003eisolates were collected from cases of bloodstream infections after routine diagnostic specimen processing, which included species identification and antimicrobial susceptibility testing (AST) using the VITEK\u003csup\u003e®\u003c/sup\u003e2 system (bioMérieux, France). Patient demographic, epidemiological, clinical and microbiological data were retrospectively collected from diagnostic laboratory databases and patient records. Isolate infection type (SAB or SAIE) was assigned based on the patient’s final clinical diagnosis, with the assistance of a clinician.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMolecular species confirmation and virulence characterisation\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eSeventy-seven non-repeat \u003cem\u003eS. aureus\u003c/em\u003e bloodstream isolates were streaked onto 5% sheep blood agar (MediaMage, SA) and incubated for 24 h at 37°C (Vacutec, UK). Thereafter, a single pure colony was inoculated into 5 mL sterile Brain Heart Infusion broth (LabM, UK) and incubated with shaking (Stuart Orbital Incubator, UK) for 24 h at 37°C. Total genomic DNA extraction was performed following the boiling method, with modifications (Barbosa et al., 2016). Briefly, phosphate-buffered saline [PBS, pH 7.2 (Thermo Scientific, USA)] was used instead of a detergent-based lysis buffer. Cultures were centrifuged three times (MC-24\u003csup\u003e®\u003c/sup\u003e Touch, Benchmark, USA): initially at 5,500 × g for 5 s, followed by two additional centrifugation and PBS (Thermo Scientific, USA) wash steps at 5,500 × g for 5 min. Lastly, a sonication step (Transsonic 460, USA) of 15 min at 35 kHz was incorporated to improve cell lysis.\u003c/p\u003e\n\u003cp\u003eA species identification multiplex polymerase chain reaction (M-PCR) assay was performed to confirm isolates as\u003cem\u003e\u0026nbsp;S. aureus\u0026nbsp;\u003c/em\u003eand to differentiate methicillin-resistant \u003cem\u003eS. aureus\u003c/em\u003e (MRSA) from methicillin-sensitive \u003cem\u003eS. aureus\u003c/em\u003e (MSSA) based on the presence of the methicillin-resistance gene (\u003cem\u003emecA\u003c/em\u003e). The \u003cem\u003eS. aureus\u003c/em\u003e isolates were screened for multiple virulence genes previously associated with SAIE, including cytolytic toxins, exoenzymes, regulatory elements, SAgs, secretable expanded repertoire adhesive molecules (SERAMs) and microbial surface components recognising adhesive matrix molecules (MSCRAMMs). Primer sequences and amplification conditions used in the conventional M-PCR assays are indicated in Table S1 provided in Online Resource 1. A CelTaq Hotstart DNA polymerase and buffer (Celtic Molecular Diagnostics, SA) master mix was prepared according to the manufacturer’s instructions. The \u003cem\u003eS. aureus\u003c/em\u003e ATCC 33591, 29213, 700699, 25923, 24213 and in-house controls were used in the identification and virulence gene detection M-PCR assays, with results interpreted according to expected amplicon band sizes for each target gene, as detailed in Table S1 in Online Resource 1.\u003c/p\u003e\n\u003cp id=\"_Toc182790097\"\u003e\u003cstrong\u003eEvaluation of \u003cem\u003eS. aureus\u003c/em\u003e phenotypic biofilm formation\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eBiofilm formation was assessed using the crystal violet assay as previously described (Merritt et al., 2005), with modifications that included culturing in 1% glucose-supplemented tryptic soy broth (Oxoid, UK), heat fixation (ProBlot 12S, Labnet, USA) at 65°C for 1 h prior to staining and the use of PBS (Thermo Scientific, USA) for washing. The \u003cem\u003eS. aureus\u003c/em\u003e ATCC 12600 was included as a reference strain. Biofilm biomass was quantified by measuring the optical density (OD) at 550 nm (OD₅₅₀) using a PR 4100 Absorbance Microtiter Plate Reader (BioRad, USA). The OD was measured using the following formula: OD cut-off (ODc) = Average OD of negative control + [3 × standard deviation (SD) of the negative control]. The final OD used to characterise biofilm formation was calculated as average isolate OD – ODc. Isolates were categorised as non (OD ≤ ODc), weak (ODc \u0026lt; OD ≤ 2 × ODc), moderate (2 × ODc \u0026lt; OD ≤ 4 × ODc) or strong (4 × ODc \u0026lt; OD) biofilm formers.\u003c/p\u003e\n\u003cp id=\"_Toc182790098\"\u003e\u003cstrong\u003ePulsed-field gel electrophoresis genotyping\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe genetic relatedness of the \u003cem\u003eS. aureus\u0026nbsp;\u003c/em\u003eisolates was assessed using pulsed-field gel electrophoresis (PFGE) with the \u003cem\u003eS. aureus\u003c/em\u003e ATCC 12600 strain as a size standard. Plug preparation was done according to McDougal et al. (2003) and the CHEF-DR\u003csup\u003e®\u003c/sup\u003e III protocol (BioRad, USA). Genomic DNA was digested with \u003cem\u003eSmaI\u003c/em\u003e (Thermo Scientific, USA) and resolved on a 1.2% (m/v) Seakem agarose gel (Lonza, USA) stained with ethidium bromide [250 μL of 10 mg/mL (Sigma-Aldrich, USA)]. The run conditions were as follows: 21 h at 14°C with an interval of 5-40 s linear at a constant angle of 120° and a voltage of 200-220 V. Gel images were analysed using GelCompar II (Applied Maths, Belgium) with cluster analysis performed using the Dice coefficient and the dendrogram constructed using unweighted pair group method with arithmetic mean. An ≥80% similarity threshold was used to define and categorise pulsotypes as major (≥5 isolates), minor (\u0026lt;5 isolates) or singletons.\u003c/p\u003e\n\u003cp id=\"_Toc182790099\"\u003e\u003cstrong\u003eWhole genome sequencing of selected \u003cem\u003eS. aureus\u0026nbsp;\u003c/em\u003eisolates\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eDue to the high cost of whole-genome sequencing (WGS) in SA, only 12 representative\u0026nbsp;\u003cbr\u003e\u003cem\u003eS. aureus\u003c/em\u003e isolates (6 SAB, 6 SAIE) were selected for this analysis. The selection aimed to capture phenotypic and genotypic diversity. Thus, isolates were considered based on AST profiles [fully susceptible to multidrug resistance (MDR)], number of virulence genes detected (low to high), biofilm-forming capacity (none to strong), patient outcome (a fatal case) and PFGE clustering to represent major clusters, minor clusters, singletons and one untypable isolate. The Quick-DNA\u003csup\u003eTM\u003c/sup\u003e Fungal/Bacterial Miniprep Kit (Zymo Research, USA) was used for DNA extraction according to the manufacturer’s instructions. The DNA quality (A260/A280 ≥1.8) was verified using a nano\u003csup\u003e\u0026nbsp;\u003c/sup\u003espectrophotometer (Labtron, UK) and submitted to the National Institute for Communicable Diseases (NICD), SA, for WGS. Multiplexed, paired-end libraries were prepared using the Nextera DNA Flex Kit (Illumina, USA) and sequenced at 100x coverage and 2 x 150 bp read length using the NextSeq 2000 (Illumina, USA) platform. Raw reads were examined for quality [FastQC 0.12.0 software (Babraham Bioinformatics, UK)], trimmed and assembled with CLC Genomics Workbench 24.0.1 (Bio-Qiagen, USA) and SPAdes 3.15.4 (Prjibelski et al., 2020). Annotation was performed using the Jekesa pipeline (Kwenda et al., 2020). Species confirmation and characterisation of AMR, virulence, plasmids, mobile genetic elements (MGEs) and genotyping were conducted using the following Centre for Genomic Epidemiology tools: SpeciesFinder (Larsen et al., 2014), ResFinder 4.6.0 (Bortolaia et al., 2020), VirulenceFinder 2.0 (Joensen et al., 2014), MGEFinder (Johansson et al., 2020), PlasmidFinder 2.1 (Carattoli et al., 2014), MLST 2.0 (Larsen et al., 2012), spaTyper (Bartels et al., 2014) and SCC\u003cem\u003emec\u003c/em\u003eFinder 1.2 (Kaya et al., 2018). Supplementary databases used included the Comprehensive Antibiotic Resistance Database (Alcock et al., 2023) and the Virulence Factor Database (Liu et al., 2022). Pairwise nucleotide polymorphism (SNP) differences were determined using the Split Kmer Analysis toolkit (Liu et al., 2022).\u003c/p\u003e\n\u003cp id=\"_Toc182790100\"\u003e\u003cstrong\u003eStatistical analysis\u003c/strong\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eContinuous variables were summarised as means (range) and medians [interquartile range (IQR)], while categorical data were reported as frequencies, proportions and 95% confidence intervals (CIs). Group comparisons were performed using Fisher’s exact test for categorical data and the Mann-Whitney U test for continuous variables, where data did not meet the assumptions of normality. Correlations were assessed using point biserial (rpb) and Kendal tau-b (τb) non-parametric tests to explore relationships between infection type (SAB and SAIE) and continuous (biofilm OD) or categorical variables (sex, ward group and risk factors). A binary logistic regression model was used to identify independent predictors of SAIE, evaluating associations with clinical characteristics including intravenous drug use (IVDU), human immunodeficiency virus (HIV) status and hepatitis C co-infection. Statistical analyses were performed using STATA 16.0 (StataCorp, USA), with two-tailed P \u0026lt; 0.05 considered statistically significant and P \u0026lt; 0.01 or P \u0026lt; 0.001 interpreted as indicating stronger evidence against the null hypothesis.\u0026nbsp;\u003c/p\u003e"},{"header":"RESULTS","content":"\u003cp\u003e\u003cstrong\u003eDemographical and clinical characteristics\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe majority [70.1% (54/77)] of the \u003cem\u003eS. aureus\u0026nbsp;\u003c/em\u003eisolates were SAB, while SAIE accounted for 29.9% (23/77) of the study isolates. The patient demographic and clinical characteristics are presented in Table 1. Isolates with incomplete data for specific variables were excluded from relevant analyses, resulting in data point variability. A significant association was found between infection type and sex (P \u0026lt; 0.001), with SAIE occurring predominantly among male patients [95.7% (22/23)]. The age of SAIE patients ranged from 22 to 45 years [median = 33, IQR = 30-36], while SAB patients ranged from 4 days to 76 years (median = 32, IQR = 23.5-41). Table 2 summarises the logistic regression results for predictors of SAIE. The model was statistically significant (\u0026chi;\u0026sup2; = 14.54, P \u0026lt; 0.01) and explained 26.2% of the variance in infection type. Recreational IVDU emerged as a strong predictor of SAIE (odds ratio = 7.46, 95% CI: 1.24\u0026ndash;45.05, P \u0026lt; 0.05), which aligned with univariate findings of PWID-SAIE association (\u0026tau;b = 0.55, P \u0026lt; 0.001). No significant associations were observed for HIV or hepatitis C after adjusting for IVDU.\u003c/p\u003e\n\u003cp\u003e\u003cem\u003e[Insert Table 1 near here]\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003e\u003cem\u003e[Insert Table 2 near here]\u003c/em\u003e\u003c/p\u003e\n\u003cp id=\"_Toc182790103\"\u003e\u003cstrong\u003eAntimicrobial resistance profiles\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAll isolates, excluding one SAB isolate, had phenotypic AST data available. Multidrug resistance, defined as resistance to \u0026ge;3 antimicrobial classes (Garrine et al., 2023), was observed in 19.7% (15/76) of the isolates, with a higher rate in SAB [24.5% (13/53)] than SAIE [8.7% (2/23)], though not statistically significant. Molecular screening of the \u003cem\u003emecA\u0026nbsp;\u003c/em\u003egene showed that 13% [10/77 (9 SAB, 1 SAIE)] of isolates were MRSA, largely consistent with AST, except for two phenotypic MRSA isolates lacking \u003cem\u003emecA\u003c/em\u003e and one \u003cem\u003emecA\u003c/em\u003e-positive isolate appearing susceptible. While overall resistance to gentamicin and clindamycin was low, significantly higher rates were observed in the SAB group [18.9% (10/53) and 20.8% (11/53), respectively] compared to the SAIE group (0%; P \u0026lt; 0.05). Inducible clindamycin resistance (ICR) was detected exclusively in SAB isolates [11.3% (6/53)], indicative of an inducible macrolides, lincosamides and streptogramin B (MLSB) resistance phenotype. Benzylpenicillin [79.0% (60/76)] and trimethoprim/sulfamethoxazole [TMP/SMX; 51.3% (39/76)] resistance were most frequent, while resistance to the remaining antimicrobials ranged from 1.3% (1/76) to 17.1% (13/76) and are detailed in Fig. 1. All isolates were susceptible to ampicillin, cefoxitin, fusidic acid, linezolid, mupirocin, streptomycin, teicoplanin, tigecycline and vancomycin.\u003c/p\u003e\n\u003cp\u003e\u003cem\u003e[Insert Fig. 1 near here]\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eVirulence gene distribution and biofilm-forming capacity\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAll 77 isolates (54 SAB, 23 SAIE) were assessed for virulence-associated traits, including the presence of key virulence genes and biofilm formation. The majority of isolates harboured 10 or more virulence genes [53.7% (29/54) SAB; 60.9% (14/23) SAIE], with Fig. 2 illustrating virulence gene distributions by infection type. All isolates harboured \u003cem\u003eicaA\u003c/em\u003e and \u003cem\u003eisdB,\u003c/em\u003e with frequent co-occurrence of \u003cem\u003esspB\u003c/em\u003e and/or \u003cem\u003escpA\u003c/em\u003e observed in 88.9% (48/54) of SAB and 91.3% (21/23) of SAIE isolates. Adhesion gene combinations involving \u003cem\u003efnbpA\u003c/em\u003e and \u003cem\u003eisdB\u003c/em\u003e were common, with \u003cem\u003efnbpA\u003c/em\u003e and \u003cem\u003eisdB\u003c/em\u003e present in 79.6% (43/54) of SAB and 78.3% (18/23) of SAIE, while \u003cem\u003eclfA\u003c/em\u003e, \u003cem\u003efnbpA\u003c/em\u003e and \u003cem\u003eisdB\u003c/em\u003e were present in 75.9% (41/54) of SAB and 60.9% (14/23) of SAIE. Most isolates [77.8% (42/54) SAB; 73.9% (17/23) SAIE] harboured all three exoenzyme genes (\u003cem\u003escpA\u003c/em\u003e, \u003cem\u003esspB\u003c/em\u003e, \u003cem\u003evWbp\u003c/em\u003e), while most carried no PTSAg genes [68.5% (37/54) SAB; 69.6% (16/23) SAIE]. The majority of SAB [44.4% (24 /54)] and SAIE [39.1% (9/23)] isolates harboured neither of the two cytolytic toxins (\u003cem\u003epvl\u003c/em\u003e and \u003cem\u003ehlb\u003c/em\u003e). The most common toxin gene combinations present were as follows:\u003cem\u003e\u0026nbsp;\u003c/em\u003ei)\u003cem\u003e\u0026nbsp;hlb\u003c/em\u003e and \u003cem\u003epvl\u0026nbsp;\u003c/em\u003e[27.8% (15/54) SAB; 34.8% (8/23) SAIE] and ii) the \u003cem\u003eegc\u003c/em\u003e encompassing \u003cem\u003eseg\u003c/em\u003e, \u003cem\u003esei\u003c/em\u003e, \u003cem\u003esem\u003c/em\u003e, \u003cem\u003esen\u003c/em\u003e, \u003cem\u003eseo\u0026nbsp;\u003c/em\u003eand sometimes \u003cem\u003esel-u\u003c/em\u003e [22.2% (12/54) SAB; 26.1% (6/23) SAIE]. No significant difference was observed in the overall possession of individual virulence genes (P \u0026gt; 0.05) or mean number of virulence genes per isolate (mean = 10, SD = 3.6-3.9, P \u0026gt; 0.05). Overall, 89.6% (69/77) of isolates demonstrated biofilm-forming capacity (Table 3). While strong biofilm formation was more frequent in SAIE [52.2% (12/23)] than SAB [33.3% (18/54)], the overall association between infection type and biofilm category was not significant (P \u0026gt; 0.05).\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cem\u003e[Insert Fig. 2 near here]\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003e\u003cem\u003e[Insert Table 3 near here]\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003ePhylogenetic clustering\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThree major pulsotypes, 15 minor pulsotypes, 26 singletons and two untypable SAB isolates were identified (Fig. 3). Significant associations were found between specific pulsotypes and several genes [\u003cem\u003emecA, cna, eap, egc, hlb, pvl\u003c/em\u003e, \u003cem\u003esdre\u003c/em\u003e (P \u0026le; 0.001)], as well as between pulsotypes and AMR [ciprofloxacin, clindamycin, erythromycin, gentamicin, oxacillin, tetracycline, TMP/SMX (P \u0026lt; 0.05); moxifloxacin (P \u0026lt; 0.01)]. Notably, pulsotypes K and O, both \u003cem\u003emecA\u003c/em\u003e-positive, demonstrated resistance to all of the above-mentioned antimicrobials, except TMP/SMX, while pulsotypes E, H\u0026ndash;J and P were exclusively \u003cem\u003epvl\u003c/em\u003e-positive.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cem\u003e[Insert Fig. 3 near here]\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eGenomic characteristics of representative isolates\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe 12 representative \u003cem\u003eS. aureus\u003c/em\u003e isolates revealed diverse genomic characteristics. Four isolates (SA51, SA53, SA5A and SA12A) demonstrated high genetic similarity, with a mean SNP value of 151 (116 to 175). The genomic similarity between the 12 representative isolates, generated using Proksee (Grant et al., 2023), is shown in Fig. 4. Isolate typing revealed 11 distinct staphylococcal protein A (\u003cem\u003espa\u003c/em\u003e) types and eight different sequence types (STs) across seven clonal complexes (CCs). The most common \u003cem\u003espa\u003c/em\u003e type was t355 [16.7% (2/12); both SAIE], while ST152 was predominant [33.3% (4/12); 1 SAB, 3 SAIE]. Among all representative isolates, 58.3% (7/12) belonged to just two CCs (CC152 and CC8). Two MRSA SAB isolates carried staphylococcal cassette chromosome methicillin (SCC\u003cem\u003emec\u003c/em\u003e) types III (3A) and IVd (2B), while all isolates harboured at least one plasmid, with 83.3% (10/12) carrying multiple plasmid replication protein (Rep) genes (\u003cem\u003erep\u003c/em\u003e). The most common plasmid types were Inc18/Rep3, with \u003cem\u003erep\u003c/em\u003e5a_1 and \u003cem\u003erep\u003c/em\u003e16_3 present in 58.3% [7/12 (2 SAB, 5 SAIE)] of isolates. Insertion sequences (IS) were identified in 58.3% [7/12 (5 SAB, 2 SAIE)] of isolates, with IS\u003cem\u003eSau3\u003c/em\u003e most prevalent in 25% [3/12 (1 SAB, 2 SAIE)]. In contrast, composite transposons (CNs), specifically CN_2257_IS\u003cem\u003eSau6\u003c/em\u003e and CN_12274_IS\u003cem\u003eSau6\u003c/em\u003e, were only harboured by one SAB isolate. Table S2 (Online Resource 1) summarises the overall WGS results, including STs, CCs, mobilome, resistome and virulome identified in the representative SAB and SAIE isolates, while Table S3 (Online Resource 1) indicates the strain typing results of individual representative isolates.\u003c/p\u003e\n\u003cp\u003eThe most prevalent AMR genes and mechanisms identified included: the multidrug efflux transporter (\u003cem\u003emepA\u003c/em\u003e) and tetracycline efflux major facilitator superfamily (MFS) transporter [\u003cem\u003etet\u003c/em\u003e(38)] present in 100% of the isolates, followed by penicillin-hydrolysing class A \u0026beta;-lactamase (\u003cem\u003eblaZ\u003c/em\u003e) and penicillinase repressor (\u003cem\u003eblaI\u003c/em\u003e) in 91.7% [11/12 (5 SAB, 6 SAIE)]. The gentamicin resistance \u003cem\u003eaac\u003c/em\u003e(6\u0026apos;)\u003cem\u003e-Ie/aph\u003c/em\u003e(2\u0026apos;\u0026apos;)\u003cem\u003e-Ia\u003c/em\u003e gene, as well as the MLSB cross-resistance genes \u003cem\u003eerm\u003c/em\u003e(ACT), were observed exclusively in SAB isolates [50% (3/6)]. Biocide and heavy metal stress response genes observed included: the multidrug efflux MFS transporter (\u003cem\u003elmrS\u003c/em\u003e), linked to resistance against macrolides and phenicols, which was present in 100% of the isolates, followed by cadmium resistance transporter D (\u003cem\u003ecadD\u003c/em\u003e), present in 91.7% [11/12 (5 SAB, 6 SAIE)]. Adhesion genes, crucial for colonisation and biofilm formation, were widely detected with the autolysin (\u003cem\u003eatl\u003c/em\u003e), elastin binding protein (\u003cem\u003eebp\u003c/em\u003e), \u003cem\u003efnbpA\u003c/em\u003e,\u003cem\u003e\u0026nbsp;icaACR\u003c/em\u003e,\u003cem\u003e\u0026nbsp;\u003c/em\u003eand \u003cem\u003espa\u003c/em\u003e genes present in 100% of isolates. Enzymatic virulence genes were extensively represented with 100% of isolates harbouring glycerol ester hydrolase (\u003cem\u003egeh\u003c/em\u003e), hyaluronate lyase (\u003cem\u003ehysA\u003c/em\u003e), lipase (\u003cem\u003elip\u003c/em\u003e), \u003cem\u003enuc\u003c/em\u003e, serine V8 protease (\u003cem\u003esspABC\u003c/em\u003e), Coa (\u003cem\u003ecoa\u003c/em\u003e) gene and zinc metalloproteinase aureolysin (\u003cem\u003eaur\u003c/em\u003e). The toxin virulence gene profiles, including enterotoxins, exfoliative toxins, exotoxins, haemolysins and leukocidins, revealed diverse representation across isolates. The alpha-haemolysin (\u003cem\u003ehly\u003c/em\u003e/\u003cem\u003ehla\u003c/em\u003e), delta haemolysin (\u003cem\u003ehld\u003c/em\u003e), and bi-component gamma-haemolysin (Hlg) subunits A and B [\u003cem\u003ehlg\u003c/em\u003e (\u003cem\u003ehlgA\u003c/em\u003e and \u003cem\u003ehlgB\u003c/em\u003e)] genes were present in 100% of the isolates, while the PVL bi-component subunit F and S [\u003cem\u003elukFS-PV\u003c/em\u003e (1 SAB, 3 SAIE)] were present in 33.3% (4/12) of the isolates. All isolates harboured the type VII secretion system (T7SS) accessory factor A gene (\u003cem\u003eesaAG\u003c/em\u003e), \u003cem\u003eessABC\u003c/em\u003e and \u003cem\u003eesxA\u003c/em\u003e.\u003cem\u003e\u0026nbsp;\u003c/em\u003eThe WGS AMR and virulence profiles of each representative SAB and SAIE isolate are illustrated in Fig. 5.\u0026nbsp;\u003c/p\u003e"},{"header":"DISCUSSION","content":"\u003cp\u003eInfective endocarditis is considered a rare manifestation of SAB; however, 29.9% of SAB cases in this study were linked to SAIE, exceeding global estimates ranging from as low as 6% in Asia to around 15% in SA and up to 27% in Switzerland (John et al., \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e2024\u003c/span\u003e; Ngiam et al., \u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e2024\u003c/span\u003e; Papadimitriou-Olivgeris et al., \u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). Public hospitals in Gauteng, serving around 77.6% of the province\u0026rsquo;s population, predominantly care for socioeconomically disadvantaged patients with higher rates of immunodeficiency, comorbidities and IVDU, factors that may have contributed to the observed overrepresentation of SAIE (Stats SA, \u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). The data suggested demographic disparities, with SAIE cases showing a higher male predominance (95.7%) compared to the 60\u0026ndash;70% typically reported in LMICs and HICs (Ahtela et al., \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Pecoraro et al., \u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). Additionally, both SAB and SAIE mainly affected younger adults (25\u0026ndash;44 years), aligning with SA data (Pecoraro et al., \u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; John et al., \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e2024\u003c/span\u003e), but contrasting with HICs, where cases mainly occur in those over 60 years (Ahtela et al., \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Papadimitriou-Olivgeris et al., \u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). These patterns likely reflect the influence of socioeconomic and healthcare challenges in SA [poverty, limited healthcare access, HIV, tuberculosis (TB), prior rheumatic heart disease and IVDU] that often disproportionately affect males in LMICs and drive earlier disease onset (de Villiers, \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Pecoraro et al., \u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). In contrast, HICs trends are shaped by ageing populations with higher burdens of degenerative valvular disease and HA risk (Cahill et al., \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e2017\u003c/span\u003e), while oestrogen\u0026rsquo;s reported cardioprotective effects may partly explain the low representation of female SAIE cases observed (Dohmen et al., \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e2016\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe strong SAIE\u0026ndash;PWID association observed reflects how non-sterile injection practices introduce pathogens and endocardial-damaging particles, while illicit drug-induced immunosuppression further exacerbates PWID health risks (Masters et al., \u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e2025\u003c/span\u003e). However, this study\u0026rsquo;s high prevalence of PWIDs (29.5%), over three times that of a 2024 SA study (9.5%) (John et al., \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e2024\u003c/span\u003e), combined with multiple comorbidities and co-infections, highlights the substantial health burden in this vulnerable population. The distribution of \u003cem\u003eS. aureus\u003c/em\u003e isolates across hospitals and wards highlighted potential epidemiological and HA patterns. Nearly half (49.4%) of the \u003cem\u003eS. aureus\u003c/em\u003e isolates were likely community-associated (CA), inferred from the high proportion originating from emergency wards. Speculatively, the concentration of SAIE and PWID cases in the emergency ward (P\u0026thinsp;\u0026lt;\u0026thinsp;0.001) may reflect delayed care-seeking among PWIDs due to stigma, limited healthcare access or concerns about legal and social repercussions (Masters et al., \u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e2025\u003c/span\u003e). Conversely, SAB occurred significantly more often in high-dependency wards (P\u0026thinsp;\u0026lt;\u0026thinsp;0.05), consistent with the elevated infection risk associated with critical illness, invasive procedures and extended hospitalisation (Samuel et al., \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e2023\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eMultidrug resistance remains an ever-present challenge in managing bacterial infections, with SAB MDR rates from this study comparable to that of a 2023 study from another LMIC, Mozambique (25%) (Garrine et al., \u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). While the study\u0026rsquo;s SAB (16.7%) MRSA prevalence aligned with Africa\u0026rsquo;s regional mean of 18% (Haindongo et al., \u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e2023\u003c/span\u003e), the lower SAIE MRSA rate (4.4%) contrasted with higher rates of 25\u0026ndash;43% reported in Asia and the USA (Kanyo et al., \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e2021\u003c/span\u003e; Ngiam et al., \u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). The lower resistance rates observed in SA may be attributed to improved infection control and antimicrobial stewardship initiatives (Segal et al., \u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). The TMP/SMX resistance rates (51.3%), well above the 19% reported in a 2017 SA study, may be driven by routine use as a cost-effective first-line agent and HIV-related prophylaxis outlined by SA treatment guidelines (Moodley and Perovic, \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e2017\u003c/span\u003e; Takuva and Nabyoma, 2017). Gentamicin, previously part of SAB and SAIE standard treatment recommendations, is now largely avoided due to nephrotoxicity concerns and limited clinical benefit, except in cases of prosthetic valve IE (Habib et al., \u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). Conversely, clindamycin remains an alternative for severe staphylococcal infections, particularly in penicillin-allergic patients and for IE prophylaxis during dental procedures (National Department of Health, \u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e2019\u003c/span\u003e). Given the historical and current use of gentamicin and clindamycin in SA, the absence of resistance in SAIE isolates compared to SAB may reflect their predominantly CA origin and limited prior antimicrobial exposure, unlike the more HA SAB isolates; however, further research is needed to clarify this discrepancy. The detection of ICR exclusively among SAB isolates highlights the need for routine testing, as undetected inducible MLSB phenotypes may evolve into constitutive forms under treatment pressure, increasing the risk of therapeutic failure (Memariani et al., \u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). While few studies have examined the AMR profiles of SAIE isolates, in this study, resistance among SAIE was generally lower than previously reported in another LMIC (Gupta et al., \u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e2021\u003c/span\u003e). The lower overall resistance rates observed in SAIE isolates might reflect the metabolic costs of maintaining broad-spectrum AMR mechanisms. In the transition from SAB to SAIE, it is plausible that \u003cem\u003eS. aureus\u003c/em\u003e may reduce its resistance burden to optimise virulence fitness and the ability to invade and persist in the more stringent endocardial environment (Beceiro et al., \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e2013\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eBoth SAB and SAIE isolates displayed similarly robust virulence potential. The high prevalence of adhesion (\u003cem\u003eclfA\u003c/em\u003e, \u003cem\u003ecna\u003c/em\u003e, \u003cem\u003eeap\u003c/em\u003e, \u003cem\u003eicaA\u003c/em\u003e, \u003cem\u003eisdB\u003c/em\u003e and \u003cem\u003efnbpA)\u003c/em\u003e and exoenzyme-associated (\u003cem\u003escpA\u003c/em\u003e, \u003cem\u003esspB\u003c/em\u003e and \u003cem\u003evWbp\u003c/em\u003e) genes was expected, given their importance in promoting bacterial adhesion, immune evasion, nutrient acquisition and biofilm modulation in invasive \u003cem\u003eS. aureus\u003c/em\u003e infections (Kinney et al., \u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e2022a\u003c/span\u003e; Kinney et al., \u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e2022b\u003c/span\u003e). Although both infection types showed a high capacity for strong biofilm formation, SAIE isolates more often produced particularly robust biofilms. However, despite links to invasive disease severity and endocardial persistence, the lack of correlation between biofilm strength and infection type supports evidence that biofilm formation alone cannot predict IE development, serving as just one of many factors influencing infection outcomes (Bouchiat et al., \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). The lack of significant differences in virulence gene distributions or biofilm formation suggests that the ability to cause severe invasive disease may be an inherent trait of most \u003cem\u003eS. aureus\u003c/em\u003e strains. Consistent with this study\u0026rsquo;s findings, Tristan et al. (\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e2012\u003c/span\u003e) found no distinct virulence genotypes distinguishing SAIE from SAB, while Bastien et al. (\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e2023\u003c/span\u003e) reported no differences in adhesion or IE propensity in murine and mechanical models. These observations suggest that specific virulence factors are unlikely to serve as reliable markers for SAIE risk. If specific determinants of SAIE development risk do exist, they are unlikely to be driven by a single genomic trait; rather, more likely arising from the interplay of multiple biological processes that converge on a shared phenotype - an increased propensity to cause SAIE. Thus, environmental, genetic and host-related risk factors (comorbidities, immune status and at-risk behaviour) may ultimately play a greater role in driving disease progression.\u003c/p\u003e \u003cp\u003eGenotyping revealed considerable genetic diversity across both SAB and SAIE isolates, with no clear pulsotype-based distinction, indicating infections arose from diverse backgrounds rather than a single clonal lineage, as supported by WGS and consistent with previous studies (Bouchiat et al., \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2015\u003c/span\u003e; Lilje et al., \u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e2017\u003c/span\u003e). The identification of closely related isolates among PWIDs raised concerns about potential outbreak risks in this vulnerable group, linked to the circulating endemic PVL-positive ST152/CC152 lineage, previously implicated in outbreaks among SA gold miners in 2017 (Ismail et al., \u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). The major African MSSA ST152 clone, which was prevalent among SAIE isolates in this study, is associated with invasive infections and increased SAIE severity, likely driven by its consistent PVL-positive nature, a trait absent from other STs in this study (Lawal et al., \u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). In contrast, the pandemic CC8 was exclusively associated with SAB isolates, including well-known HA-MRSA clones such as ST239, ST508 and ST612 (Singh-Moodley et al., \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e2020\u003c/span\u003e; Lawal et al., \u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e2022\u003c/span\u003e; Hetsa et al., \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). Interestingly, CCs traditionally linked to SAIE, including CC5, CC8, CC15 and CC45, were only detected among SAB isolates (Tristan et al., \u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e2012\u003c/span\u003e; Bouchiat et al., \u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e2015\u003c/span\u003e). This variation may have reflected regional differences in clonal distribution or suggested that SAIE isolates in SA belong to a broader range of CCs than elsewhere (Lawal et al., \u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e2022\u003c/span\u003e; Hetsa et al., \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e2024\u003c/span\u003e). The presence of genetically related isolates from both SAB and SAIE cases (SA5A and SA51, both ST152-t355) suggests that all SAB isolates, regardless of genotype, may have the potential to cause SAIE under opportunistic conditions. However, further epidemiological studies with larger WGS sample sizes are needed to confirm the associations in SA clinical settings.\u003c/p\u003e \u003cp\u003eRepresentative SAB isolates harboured a wider variety of MGEs, likely influenced by their HA origin, where MGE acquisition is common (Samuel et al., \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e2023\u003c/span\u003e). The detection of SCC\u003cem\u003emec\u003c/em\u003e types III (3A) and IVd (2B) aligned with regional data as dominant SCC\u003cem\u003emec\u003c/em\u003e types (Singh-Moodley et al., \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Specifically, the Brazilian/Hungarian clone t037-ST239-MRSA-III (CC8) and ST612-MRSA-IV clone (CC8) continued to circulate within the study setting, reflecting the endemic status (Singh-Moodley et al., \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e2020\u003c/span\u003e). Whole-genome sequencing provided a detailed analysis of AMR genes present, which aligned with phenotypic AST results. The \u003cem\u003eerm\u003c/em\u003e genes associated with clindamycin and MLSB resistance were often found on MGEs, while \u003cem\u003eerm\u003c/em\u003e(AC) genes in the representative isolates were occasionally chromosomally encoded, likely explaining the variable clindamycin resistance observed among SAB isolates (Memariani et al., \u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e2021\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eContrary to the low toxin presence in the M-PCR assay results, exotoxins and haemolysins were more dominant in the subset of WGS isolates. Fully functional leukocidins, including the complete bicomponent PVL (\u003cem\u003elukFS-PV\u003c/em\u003e) in 33.33% (4/12) of isolates and leukocidin ED (\u003cem\u003elukED\u003c/em\u003e) in 41.67% (5/12) of isolates, were observed. The HlgAB subunits were present in all isolates, while only 67% (8/12) of isolates carried the \u003cem\u003ehlgC\u003c/em\u003e gene necessary for HlgCB activity. The findings indicated variability in leukocidin composition and suggested potential diverse functional capabilities among the representative \u003cem\u003eS. aureus\u003c/em\u003e isolates. The universal presence of the \u003cem\u003eicaAC\u003c/em\u003e genes, along with the high prevalence of the \u003cem\u003eicaB\u003c/em\u003e gene [91.7% (11/12)], suggested a robust capacity for biofilm initiation and maturation during invasive infections (Peng et al., \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e2022\u003c/span\u003e). While present in both groups, nearly all SAIE isolates (excluding one) harboured the complete set of 12 T7SS genes, compared to the more variable presence in SAB. This complete T7SS repertoire in SAIE suggests enhanced colonisation, immune evasion and interbacterial competition with T7SS gene content variation likely influenced by host-derived signals that modulate T7SS activation, which may differ between cardiac tissue and bloodstream environments (Boardman et al., \u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e2023\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThis study provides a comprehensive comparison of the phenotypic, genotypic and patient characteristics of SAB and SAIE isolates within a SA context. However, the observational retrospective nature of this study posed inherent challenges. The modest sample size and uneven distribution of infection types likely reduced statistical power to detect smaller effects, while limited or absent clinical information introduced a potential risk of infection type misclassification. Nonetheless, these limitations reflect the real-world data collection constraints typical of LMIC public health sector research. Future studies should explore the relationship between patient characteristics, \u003cem\u003eS. aureus\u003c/em\u003e infection dynamics and the SAB to SAIE progression in LMICs. Continued surveillance is essential to monitor and address the unique challenges posed by \u003cem\u003eS. aureus\u003c/em\u003e infections in LMICs.\u003c/p\u003e"},{"header":"CONCLUSION","content":"\u003cp\u003eThe study provided valuable insights into the AMR and pathogenic profiles of invasive \u003cem\u003eS. aureus\u003c/em\u003e isolates from public healthcare settings in Gauteng, SA. No distinct phenotypic or genetic markers were explicitly linked to SAIE compared to SAB isolates, except for gentamicin and clindamycin resistance exclusive to SAB isolates, suggesting that all SAB isolates may possess the pathogenic potential to progress to IE. Additionally, while pathogenic traits of\u0026nbsp;\u003cem\u003eS. aureus\u003c/em\u003e are important, host factors, particularly among high-risk groups, may play a more pivotal role in predicting disease progression. The high prevalence of PWID-associated SAIE observed underscores the need for targeted public health interventions and holistic strategies to address modifiable risk factors in both SAB and SAIE management.\u0026nbsp;\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgements\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors would like to acknowledge the National Health Laboratory Service (NHLS) for funding this study. Ms Spaltman would like to acknowledge the National Research Foundation (NRF) and the Oppenheimer Memorial Trust (OMT) for their financial support. The views expressed in this study and the conclusions formulated are the authors’ and are not to be attributed to those of the NHLS, NRF or OMT.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study was supported by the National Health Laboratory Service (NHLS).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDeclaration of competing interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor Contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eLDS:\u003c/strong\u003e Conceptualisation and study design; investigation; methodology; data curation; formal analysis; writing - original draft preparation; writing - review and editing.\u0026nbsp;\u003cbr\u003e\u003cstrong\u003eTH:\u003c/strong\u003e Conceptualisation and study design; supervision; writing - review and editing.\u0026nbsp;\u003cbr\u003e\u003cstrong\u003eVU:\u003c/strong\u003e Assistance with retrospective clinical data acquisition; writing - review and editing.\u0026nbsp;\u003cbr\u003e\u003cstrong\u003eMK:\u003c/strong\u003e Technical assistance with dendrogram construction; writing - review and editing.\u0026nbsp;\u003cbr\u003e\u003cstrong\u003eAB:\u003c/strong\u003e Assistance with initial patient data collection and isolate procurement; supervision; writing - review and editing. \u003cstrong\u003eMME:\u003c/strong\u003e Conceptualisation and study design; supervision; resources; funding acquisition; writing - review and editing. All authors contributed to the article and approved the submitted version.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData availability\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe whole-genome sequencing datasets generated and analysed during this study have been deposited in the DDBJ/ENA/GenBank under BioProject number PRJNA1366126, with accession numbers SAMN53307515-SAMN53307526. All other datasets used and analysed during the current study are available from the corresponding author on reasonable request.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics declarations\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics approval\u003c/strong\u003e \u003cstrong\u003eand consent to participate\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study was performed in accordance with the principles of the Declaration of Helsinki. Ethical approval was granted by the University of Pretoria, Faculty of Health Sciences Research Ethics Committee (Reference number: 183/2023). Informed consent was waived due to the retrospective nature of the study, with all patient information de-identified and anonymised prior to analysis.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eAchoki T, Sartorius B, Watkins D, Glenn SD, Kengne AP, Oni T, Wiysonge CS, Walker A, Adetokunboh OO, Babalola TK, Bolarinwa OA, Claassens MM, Cowden RG, Day CT, Ezekannagha O, Ginindza TG, Iwu CCD, Iwu CJ, Karangwa I, Katoto PD, Kugbey N, Kuupiel D, Mahasha PW, Mashamba-Thompson TP, Mensah GA, Ndwandwe DE, Nnaji CA, Ntsekhe M, Nyirenda TE, Odhiambo JN, Oppong Asante K, Parry CDH, Pillay JD, Schutte AE, Seedat S, Sliwa K, Stein DJ, Tanser FC, Useh U, Zar HJ, Z\u0026uuml;hlke LJ, Mayosi BM, Hay SI, Murray CJL, Naghavi M (2022) Health trends, inequalities and opportunities in South Africa\u0026apos;s provinces, 1990-2019: Findings from the Global Burden of Disease 2019 study. J Epidemiol Community Health 76:471\u0026ndash;81. https://doi.org/10.1136/jech-2021-217480.\u003c/li\u003e\n\u003cli\u003eAgnello S, Wardlow LC, Reed E, Smith JM, Coe K, Day SR (2021) Clinical outcomes of daptomycin versus anti-staphylococcal beta-lactams in definitive treatment of methicillin-susceptible \u003cem\u003eStaphylococcus aureus\u003c/em\u003e bloodstream infections. Int J Antimicrob Agents 58:106363. https://doi.org/10.1016/j.ijantimicag.2021.106363.\u003c/li\u003e\n\u003cli\u003eAhtela E, Oksi J, Vahlberg T, Sipil\u0026auml; J, Rautava P, Kyt\u0026ouml; V (2021) Short- and long-term outcomes of infective endocarditis admission in adults: A population-based registry study in Finland. PLoS ONE 16:e0254553. https://doi.org/10.1371/journal.pone.0254553.\u003c/li\u003e\n\u003cli\u003eAlcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR, Wlodarski MA, Edalatmand A, Petkau A, Syed SA, Tsang KK, Baker SJC, Dave M, McCarthy MC, Mukiri KM, Nasir JA, Golbon B, Imtiaz H, Jiang X, Kaur K, Kwong M, Liang ZC, Niu KC, Shan P, Yang JYJ, Gray KL, Hoad GR, Jia B, Bhando T, Carfrae LA, Farha MA, French S, Gordzevich R, Rachwalski K, Tu MM, Bordeleau E, Dooley D, Griffiths E, Zubyk HL, Brown ED, Maguire F, Beiko RG, Hsiao WWL, Brinkman FSL, Van Domselaar G, McArthur AG (2023) CARD 2023: Expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res 51:D690\u0026ndash;d699. https://doi.org/10.1093/nar/gkac920.\u003c/li\u003e\n\u003cli\u003eBarbosa C, Nogueira S, Gadanho M, Chaves S (2016) DNA extraction: Finding the most suitable method. In: Cook N, D\u0026apos;Agostino M, Thompson KC (ed). Molecular microbial diagnostic methods 2016:135\u0026ndash;154. https:/doi.org/10.1016/B978-0-12-416999-9.00007-1.\u003c/li\u003e\n\u003cli\u003eBartels MD, Petersen A, Worning P, Nielsen JB, Larner-Svensson H, Johansen HK, Andersen LP, Jarl\u0026oslash;v JO, Boye K, Larsen AR, Westh H (2014) Comparing whole-genome sequencing with Sanger sequencing for \u003cem\u003espa\u003c/em\u003e typing of methicillin-resistant \u003cem\u003eStaphylococcus aureus\u003c/em\u003e. J Clin Microbiol 52:4305\u0026ndash;8. https://doi.org/10.1128/jcm.01979-14.\u003c/li\u003e\n\u003cli\u003eBastien S, Meyers S, Salgado-Pab\u0026oacute;n W, Giulieri SG, Rasigade J-P, Liesenborghs L, Kinney KJ, Couzon F, Martins-Simoes P, Moing VL, Duval X, Holmes NE, Bruun NE, Skov R, Howden BP, Fowler VG, Verhamme P, Andersen PS, Bouchiat C, Moreau K, Vandenesch F (2023) All \u003cem\u003eStaphylococcus aureus\u003c/em\u003e bacteraemia-inducing strains can cause infective endocarditis: Results of GWAS and experimental animal studies. J Infect 86:123\u0026ndash;133. https://doi.org/10.1016/j.jinf.2022.12.028.\u003c/li\u003e\n\u003cli\u003eBeceiro A, Tom\u0026aacute;s M, Bou G (2013) Antimicrobial resistance and virulence: A successful or deleterious association in the bacterial world? Clin Microbiol Rev 26:185\u0026ndash;230. https://doi.org/10.1128/cmr.00059-12.\u003c/li\u003e\n\u003cli\u003eBoardman ER, Palmer T, Alcock F (2023) Interbacterial competition mediated by the type VIIb secretion system. Microbiology (Reading) 169. https://doi.org/10.1099/mic.0.001420.\u003c/li\u003e\n\u003cli\u003eBortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nyk\u0026auml;senoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75:3491\u0026ndash;3500. https://doi.org/10.1093/jac/dkaa345.\u003c/li\u003e\n\u003cli\u003eBouchiat C, Moreau K, Devillard S, Rasigade J-P, Mosnier A, Geissmann T, Bes M, Tristan A, Lina G, Laurent F, Piroth L, Aissa N, Duval X, Le Moing V, Vandenesch F, Chirouze C, Curlier E, Descottes-Genon C, Hoen B, Patry I, Vettoretti L, Chavanet P, Eicher J-C, Gohier-Treuvelot S, Greusard M-C, Neuwirth C, P\u0026eacute;chinot A, Piroth L, C\u0026eacute;lard M, Cornu C, Delahaye F, Hadid M, Rausch P, Coma A, Galtier F, G\u0026eacute;raud P, Jean-Pierre H, Le Moing V, Sportouch C, Reynes J, Aissa N, Doco-Lecompte T, Goehringer F, Keil N, Letranchant L, Malela H, May T, Selton-Suty C, Bedos N, Lavigne J-P, Lechiche C, Sotto A, Duval X, Habensus EI, Iung B, Leport C, Longuet P, Ruimy R, Bellissant E, Donnio P-Y, Le Gac F, Michelet C, Revest M, Tattevin P, Thebault E, Alla F, Braquet P, Erpelding M-L, Minary L, Tubiana S, B\u0026egrave;s M, Etienne J, Tristan A, Vandenesch F, Barbas S, Delonca C, Sussmuth V, Verch\u0026egrave;re A (2015) \u003cem\u003eStaphylococcus aureus\u003c/em\u003e infective endocarditis versus bacteremia strains: Subtle genetic differences at stake. Infect Genet Evol 36:524\u0026ndash;530. https://doi.org/10.1016/j.meegid.2015.08.029.\u003c/li\u003e\n\u003cli\u003eCahill TJ, Baddour LM, Habib G, Hoen B, Salaun E, Pettersson GB, Sch\u0026auml;fers HJ, Prendergast BD (2017) Challenges in infective endocarditis. J Am Coll Cardiol 69:325\u0026ndash;344. https://doi.org/10.1016/j.jacc.2016.10.066.\u003c/li\u003e\n\u003cli\u003eCarattoli A, Zankari E, Garc\u0026iacute;a-Fern\u0026aacute;ndez A, Voldby Larsen M, Lund O, Villa L, M\u0026oslash;ller Aarestrup F, Hasman H (2014) \u003cem\u003ein silico\u003c/em\u003e detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895\u0026ndash;903. https://doi.org/10.1128/aac.02412-14.\u003c/li\u003e\n\u003cli\u003ede Villiers K (2021) Bridging the health inequality gap: An examination of South Africa\u0026rsquo;s social innovation in health landscape. Infect Dis Poverty 10:19. https://doi.org/10.1186/s40249-021-00804-9.\u003c/li\u003e\n\u003cli\u003eDohmen PM, Binner C, Mende M, Daviewala P, Etz CD, Borger MA, Misfeld M, Eifert S, Mohr FW (2016) Gender-based long-term surgical outcome in patients with active infective aortic valve endocarditis. Med Sci Monit 22:2520\u0026ndash;2527. https://doi.org/10.12659/msm.899360.\u003c/li\u003e\n\u003cli\u003eGarrine M, Costa SS, Messa A, Jr., Massora S, Vubil D, \u0026Aacute;cacio S, Nhampossa T, Bassat Q, Mandomando I, Couto I (2023) Antimicrobial resistance and clonality of \u003cbr\u003e\u003cem\u003eStaphylococcus aureus\u003c/em\u003e causing bacteraemia in children admitted to the Manhi\u0026ccedil;a District Hospital, Mozambique, over two decades. Front Microbiol 14:1208131. https://doi.org/10.3389/fmicb.2023.1208131.\u003c/li\u003e\n\u003cli\u003eGrant JR, Enns E, Marinier E, Mandal A, Herman EK, Chen C-y, Graham M, Van Domselaar G, Stothard P (2023) Proksee: In-depth characterization and visualization of bacterial genomes. Nucleic Acids Res 51:W484\u0026ndash;W492. https://doi.org/10.1093/nar/gkad326.\u003c/li\u003e\n\u003cli\u003eGupta R, Kaushal V, Goyal A, Kumar P, Gupta D, Tandon R, Mahajan A, Singla S, Singh G, Singh B, Chhabra ST, Aslam N, Wander GS, Gupta V, Mohan B (2021) Changing microbiological profile and antimicrobial susceptibility of the isolates obtained from patients with infective endocarditis \u0026ndash; The time to relook into the therapeutic guidelines. Indian Heart J 73:704\u0026ndash;710. https://doi.org/10.1016/j.ihj.2021.10.013.\u003c/li\u003e\n\u003cli\u003eHabib G, Lancellotti P, Antunes MJ, Bongiorni MG, Casalta J-P, Del Zotti F, Dulgheru R, El Khoury G, Erba PA, Iung B, Miro JM, Mulder BJ, Plonska-Gosciniak E, Price S, Roos-Hesselink J, Snygg-Martin U, Thuny F, Tornos Mas P, Vilacosta I, Zamorano JL, Group ESD (2015) 2015 ESC Guidelines for the management of infective endocarditis: The task force for the management of infective endocarditis of the European Society of Cardiology (ESC)Endorsed by: European Association for Cardio-Thoracic Surgery (EACTS), the European Association of Nuclear Medicine (EANM). Eur Heart J 36:3075\u0026ndash;3128. https://doi.org/10.1093/eurheartj/ehv319.\u003c/li\u003e\n\u003cli\u003eHaindongo EH, Ndakolo D, Hedimbi M, Vainio O, Hakanen A, Vuopio J (2023) Antimicrobial resistance prevalence of Escherichia coli and \u003cem\u003eStaphylococcus aureus\u003c/em\u003e amongst bacteremic patients in Africa: A systematic review. J Glob Antimicrob Resist 32:35\u0026ndash;43. https://doi.org/10.1016/j.jgar.2022.11.016.\u003c/li\u003e\n\u003cli\u003eHetsa BA, Asante J, Mbanga J, Ismail A, Abia ALK, Amoako DG, Essack SY (2024) Genomic characterization of methicillin-resistant and methicillin-susceptible \u003cem\u003eStaphylococcus aureus\u003c/em\u003e implicated in bloodstream infections, KwaZulu-Natal, South Africa: A pilot study. Antibiotics 13:796. https://doi.org/10.3390/antibiotics13090796.\u003c/li\u003e\n\u003cli\u003eIsmail H, Govender NP, Singh-Moodley A, van Schalkwyk E, Shuping L, Moema I, Feller G, Mogokotleng R, Strasheim W, Lowe M, Mpembe R, Naicker S, Maphanga TG, De Abreu C, Ismail F, Ismail N, Allam M, Ismail A, Singh T, Matuka O, Duba T, Perovic O (2020) An outbreak of cutaneous abscesses caused by Panton-Valentine leukocidin-producing methicillin-susceptible \u003cem\u003eStaphylococcus aureus\u003c/em\u003e among gold mine workers, South Africa, November 2017 to March 2018. BMC Infect Dis 20:621. https://doi.org/10.1186/s12879-020-05352-5.\u003c/li\u003e\n\u003cli\u003eJoensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM (2014) Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic \u003cem\u003eEscherichia coli\u003c/em\u003e. J Clin Microbiol 52:1501\u0026ndash;10. https://doi.org/10.1128/jcm.03617-13.\u003c/li\u003e\n\u003cli\u003eJohansson MHK, Bortolaia V, Tansirichaiya S, Aarestrup FM, Roberts AP, Petersen TN (2020) Detection of mobile genetic elements associated with antibiotic resistance in \u003cbr\u003e\u003cem\u003eSalmonella enterica\u003c/em\u003e using a newly developed web tool: MobileElementFinder. J Antimicrob Chemother 76:101\u0026ndash;109. https://doi.org/10.1093/jac/dkaa390.\u003c/li\u003e\n\u003cli\u003eJohn M, Richards L, Nel JS (2024) \u003cem\u003eStaphylococcus aureus\u003c/em\u003e bacteraemia cases at Helen Joseph Hospital. S Afr J Infect Dis 39. https://doi.org/10.4102/sajid.v39i1.626.\u003c/li\u003e\n\u003cli\u003eKanyo EC, Nowacki AS, Gordon SM, Shrestha NK (2021) Comparison of mortality, stroke, and relapse for methicillin-resistant versus methicillin-susceptible \u003cem\u003eStaphylococcus aureus\u003c/em\u003e infective endocarditis: A retrospective cohort study. Diagn Microbiol Infect Dis 100:115395. https://doi.org/10.1016/j.diagmicrobio.2021.115395.\u003c/li\u003e\n\u003cli\u003eKaya H, Hasman H, Larsen J, Stegger M, Johannesen TB, Alles\u0026oslash;e RL, Lemvigh CK, Aarestrup FM, Lund O, Larsen AR (2018) SCCmecFinder, a web-based tool for typing of staphylococcal cassette chromosome \u003cem\u003emec\u003c/em\u003e in \u003cem\u003eStaphylococcus aureus\u003c/em\u003e using whole-genome sequence data. mSphere 3:00612\u0026ndash;17. https://doi.org/10.1128/msphere.00612-17.\u003c/li\u003e\n\u003cli\u003eKinney KJ, Stach JM, Kulhankova K, Brown M, Salgado-Pab\u0026oacute;n W (2022a) Vegetation formation in \u003cem\u003eStaphylococcus aureus\u003c/em\u003e endocarditis inversely correlates with RNAIII and \u003cem\u003esarA\u003c/em\u003e expression in invasive clonal complex 5 isolates. Front Cell Infect Microbiol 12. https://doi.org/10.3389/fcimb.2022.925914.\u003c/li\u003e\n\u003cli\u003eKinney KJ, Tang SS, Wu X-J, Tran PM, Bharadwaj NS, Gibson-Corley KN, Forsythe AN, Kulhankova K, Gumperz JE, Salgado-Pab\u0026oacute;n W (2022b) SEC is an antiangiogenic virulence factor that promotes \u003cem\u003eStaphylococcus aureus\u003c/em\u003e endocarditis independent of superantigen activity. Sci Adv 8:eabo1072. https://doi.org/10.1126/sciadv.abo1072\u003c/li\u003e\n\u003cli\u003eKwenda S, Khumalo Z, Mtshali S, Mnyameni F, Ismail A (2020) Jekesa: An automated easy-to-use pipeline for bacterial whole genome typing, 2020. https://github.com/stanikae/jekesa. Accessed 21 Nov 2024.\u003c/li\u003e\n\u003cli\u003eLarsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pont\u0026eacute;n T, Aarestrup FM, Ussery DW, Lund O (2014) Benchmarking of methods for genomic taxonomy. J Clin Microbiol 52:1529\u0026ndash;39. https://doi.org/10.1128/jcm.02981-13.\u003c/li\u003e\n\u003cli\u003eLarsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pont\u0026eacute;n T, Ussery DW, Aarestrup FM, Lund O (2012) Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:1355\u0026ndash;61. https://doi.org/10.1128/jcm.06094-11.\u003c/li\u003e\n\u003cli\u003eLawal OU, Ayobami O, Abouelfetouh A, Mourabit N, Kaba M, Egyir B, Abdulgader SM, Shittu AO (2022) A 6-year update on the diversity of methicillin-resistant \u003cbr\u003e\u003cem\u003eStaphylococcus aureus\u003c/em\u003e clones in Africa: A systematic review. Front Microbiol 13:860436. https://doi.org/10.3389/fmicb.2022.860436.\u003c/li\u003e\n\u003cli\u003eLilje B, Rasmussen RV, Dahl A, Stegger M, Skov RL, Fowler VG, Ng KL, Kiil K, Larsen AR, Petersen A, Johansen HK, Sch\u0026oslash;nheyder HC, Arpi M, Rosenvinge FS, Korup E, H\u0026oslash;st U, Hassager C, Gill SUA, Hansen TF, Johannesen TB, Smit J, S\u0026oslash;gaard P, Skytt Andersen P, Eske-Bruun N (2017) Whole-genome sequencing of bloodstream \u003cem\u003eStaphylococcus aureus\u003c/em\u003e isolates does not distinguish bacteraemia from endocarditis. Microb Genom 3. https://doi.org/10.1099/mgen.0.000138.\u003c/li\u003e\n\u003cli\u003eLiu B, Zheng D, Zhou S, Chen L, Yang J (2022) VFDB 2022: A general classification scheme for bacterial virulence factors. Nucleic Acids Res 50:D912\u0026ndash;d917. https://doi.org/10.1093/nar/gkab1107.\u003c/li\u003e\n\u003cli\u003eMasters J, Goodman-Meza D, Russell D, Marks L, McCreary E, Jacka B, Seear K, Davis JS, Matthews G, Martinello M, Tong SYC, Dore GJ (2025) Bacterial and fungal infections in persons who inject drugs. Clin Microbiol Rev 0:e00162\u0026ndash;23. https://doi.org/10.1128/cmr.00162-23.\u003c/li\u003e\n\u003cli\u003eMcDougal LK, Steward CD, Killgore GE, Chaitram JM, McAllister SK, Tenover FC (2003) Pulsed-field gel electrophoresis typing of oxacillin-resistant \u003cem\u003eStaphylococcus aureus\u003c/em\u003e isolates from the United States: Establishing a national database. J Clin Microbiol 41:5113\u0026ndash;5120. https://doi.org/10.1128/jcm.41.11.5113-5120.2003.\u003c/li\u003e\n\u003cli\u003eMemariani M, Memariani H, Moravvej H (2021) Inducible clindamycin resistance among clinical \u003cem\u003eStaphylococcus aureus\u003c/em\u003e strains in Iran: A contemporaneous systematic review and meta-analysis. Gene Rep 23:101104. https://doi.org/10.1016/j.genrep.2021.101104.\u003c/li\u003e\n\u003cli\u003eMerritt JH, Kadouri DE, O\u0026apos;Toole GA (2005) Growing and analyzing static biofilms. Curr Protoc Microbiol 2005:1B.1. https://doi.org/10.1002/9780471729259.mc01b01s00.\u003c/li\u003e\n\u003cli\u003eMoodley A, Perovic O (2017) Characterisation of \u003cem\u003eStaphylococcus aureus\u003c/em\u003e bloodstream isolates from Gauteng and Western Cape provinces, South Africa, 2016 and 2017. Public Health Surveill Bull 16:99\u0026ndash;107. https://www.nicd.ac.za/wp-content/uploads/2018/09/Characterisation-of-Staphylococcus-aureus-bloodstream-isolates-from-Gauteng-and-Western-Cape-provinces-South-Africa-2016-and-2017.pdf. Accessed 23 Mar 2023.\u003c/li\u003e\n\u003cli\u003eNational Department of Health (2019) Essential Drugs Programme: Hospital level (Adults) Standard Treatment Guidelines and Essential Medicines List. In: National Department of Health SA editor. Pretoria, Republic of South Africa; 2019. https://knowledgehub.health.gov.za/system/files/elibdownloads/2023-04/Hospital%2520Level%2520%2528Adult%2529%25202019_v2.0.pdf. Accessed 29 Jan 2023.\u003c/li\u003e\n\u003cli\u003eNgiam JN, Koh MCY, Archuleta S, Fisher D, Chai LY-A, Sia C-H, Kong WKF, Tambyah PA (2024) Performance of risk scores in predicting infective endocarditis in patients with \u003cem\u003eStaphylococcus aureus\u003c/em\u003e bacteraemia in a prospective asian cohort. J Clin Med 13:2947. https://doi.org/10.3390/jcm13102947.\u003c/li\u003e\n\u003cli\u003ePapadimitriou-Olivgeris M, Guery B, Monney P, Senn L, Steinmetz S, Boillat-Blanco N (2024) Prevalence of infective endocarditis among patients with \u003cem\u003eStaphylococcus aureus\u003c/em\u003e bacteraemia and bone and joint infections. Microorganisms 12:342. https://doi.org/10.3390/microorganisms12020342.\u003c/li\u003e\n\u003cli\u003ePecoraro AJK, Pienaar C, Herbst PG, Poerstamper S, Joubert L, Taljaard J, Prozesky H, Janson J, Newton-Foot M, Doubell AF (2021) Causes of infective endocarditis in the Western Cape, South Africa: A prospective cohort study using a set protocol for organism detection and central decision making by an endocarditis team. BMJ Open 11:e053169. https://doi.org/10.1136/bmjopen-2021-053169.\u003c/li\u003e\n\u003cli\u003ePeng Q, Tang X, Dong W, Sun N, Yuan W (2022) A review of biofilm formation of \u003cem\u003eStaphylococcus aureus\u003c/em\u003e and its regulation mechanism. Antibiotics (Basel) 12. https://doi.org/10.3390/antibiotics12010012.\u003c/li\u003e\n\u003cli\u003ePrjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A (2020) Using SPAdes \u003cbr\u003e\u003cem\u003ede novo\u003c/em\u003e assembler. Curr Protoc Bioinformatics 70:e102. https://doi.org/10.1002/cpbi.102.\u003c/li\u003e\n\u003cli\u003eSalgado-Pab\u0026oacute;n W, Breshears L, Spaulding AR, Merriman JA, Stach CS, Horswill AR, Peterson ML, Schlievert PM (2013) Superantigens are critical for \u003cem\u003eStaphylococcus aureus\u003c/em\u003e infective endocarditis, sepsis, and acute kidney injury. mBio 4. https://doi.org/10.1128/mBio.00494-13.\u003c/li\u003e\n\u003cli\u003eSamuel P, Kumar YS, Suthakar BJ, Karawita J, Sunil Kumar D, Vedha V, Shah H, Thakkar K (2023) Methicillin-resistant \u003cem\u003eStaphylococcus aureus\u003c/em\u003e colonization in intensive care and burn units: A narrative review. Cureus 15:e47139. https://doi.org/10.7759/cureus.47139.\u003c/li\u003e\n\u003cli\u003eSegal B, Langham A, Klevansky R, Patel N, Mokoena T, Nassiep M, Ramatlo O, Ahmad A, Duse AG (2023) Analysis of the trends of methicillin-resistant \u003cem\u003eStaphylococcus aureus\u003c/em\u003e in Gauteng public hospitals from 2009 to 2018. Microbiol Spectr 11:e03623\u0026ndash;22. https://doi.org/10.1128/spectrum.03623-22.\u003c/li\u003e\n\u003cli\u003eSingh-Moodley A, Lowe M, Mogokotleng R, Perovic O (2020) Diversity of SCCmec elements and spa types in South African \u003cem\u003eStaphylococcus aureus\u003c/em\u003e mecA-positive blood culture isolates. BMC Infect Dis 20:816. https://doi.org/10.1186/s12879-020-05547-w.\u003c/li\u003e\n\u003cli\u003eStats SA (2023) General Household Survey of 2023: Statistical Release. In: Africa DoSS editor. Department of Statistics, Republic of South Africa. Statistical Release. Pretoria: Stats SA; 2023. vol. 318. https://www.statssa.gov.za/publications/P0318/P03182023.pdf. Accessed 11 Nov 2024.\u003c/li\u003e\n\u003cli\u003eTakuva SNabyoma N (2017) South African National essential medicine list adult hospital level medication review process component: HIV and AIDs. In: Health SANDo editor: South African National Department of Health; 2017. https://knowledgehub.health.gov.za/system/files/elibdownloads/2020-07/CD4%20cut-off%20for%20cotrimoxazole%20for%20OI%20prophylaxis%20in%20PLHIV_Adult%20review_16May2017.pdf. Accessed 26 Jun 2023.\u003c/li\u003e\n\u003cli\u003eTristan A, Rasigade JP, Ruizendaal E, Laurent F, Bes M, Meugnier H, Lina G, Etienne J, Celard M, Tattevin P, Monecke S, Le Moing V, Vandenesch F (2012) Rise of CC398 lineage of \u003cem\u003eStaphylococcus aureus\u003c/em\u003e among infective endocarditis isolates revealed by two consecutive population-based studies in France. PLoS ONE 7:e51172. https://doi.org/10.1371/journal.pone.0051172.\u003c/li\u003e\n\u003c/ol\u003e"},{"header":"Tables","content":"\u003cp\u003e\u003cstrong\u003eTable 1: Demographical characteristics of \u003cem\u003eStaphylococcus aureus\u003c/em\u003e bacteraemia and infective endocarditis isolate groups\u003c/strong\u003e\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"618\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" style=\"width: 180px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eCharacteristic\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 96px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eNo. of Isolates with the Characteristic [n=77 (%)]\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 210px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eNo. of Isolates with the Characteristic by Infection Type\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eOverall P Value\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eBacteraemia\u003cbr\u003e\u0026nbsp;[n=54 (%)]\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eInfective Endocarditis [n= 23 (%)]\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eSubgroup\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003e\u003cstrong\u003eP Value\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 60px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eOverall Group P Value\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"6\" style=\"width: 618px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eSex\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003e\u003csup\u003ea\u003c/sup\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eMale\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e52 (69.33)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e30 (57.69)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e22 (95.65)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" rowspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003e0.001*\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eFemale\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e23 (30.67)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e22 (42.31)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e1 (4.35)\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eUnknown\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003eN/A\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"6\" style=\"width: 618px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eAge Groups \u003csup\u003ea\u003c/sup\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003e\u0026lt;5 years\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e7 (10.14)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e7 (14.58)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e0.092\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"5\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0.049*\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003e5 years - 24 years\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e7 (10.14)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e6 (12.50)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e1 (4.76)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e0.427\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003e25 years - 44 years\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e44 (63.77)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e25 (52.08)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e19 (90.48)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e0.002*\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003e45 years - 64 years\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e8 (11.59)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e7 (14.58)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e1 (4.76)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e0.419\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003e\u0026gt;65 years\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e3 (4.35)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e3 (6.25)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e0.548\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eUnknown\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e8\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e6\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e2\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003eN/A\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"6\" style=\"width: 618px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eHospital\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003e\u003csup\u003eb\u003c/sup\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eHospital 1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e25 (32.47)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e20 (37.04)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e5 (21.74)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e0.288\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"7\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0.001*\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eHospital 2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e13 (16.88)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e13 (24.07)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e0.008*\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eHospital 3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e1 (1.30)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e1 (1.85)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e1.000\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eHospital 4\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e20 (25.97)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e7 (12.96)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e13 (56.52)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e0.000*\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eHospital 5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e8 (10.39)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e6 (11.11)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e2 (8.70)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e1.000\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eHospital 6\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e5 (6.49)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e3 (5.56)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e2 (8.70)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e0.632\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eHospital 7\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e5 (6.49)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e4 (7.41)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e1 (4.35)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e1.000\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"6\" style=\"width: 618px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eWards \u003csup\u003ea\u003c/sup\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eEmergency\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e38 (52.78)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e19 (38.78)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e19 (82.61)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e0.000*\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"4\" style=\"width: 60px;\"\u003e\n \u003cp\u003e0.004*\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eHigh dependency\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e15 (20.83)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e14 (28.57)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e1 (4.35)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e0.028*\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eGeneral\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e17 (23.61)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e14 (28.57)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e3 (13.04)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e0.234\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eOutpatient\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e2 (2.78)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e2 (4.08)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 72px;\"\u003e\n \u003cp\u003e1.000\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eUnknown\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003eN/A\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"6\" style=\"width: 618px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eRisk Factors and Clinical Conditions\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003e\u003csup\u003ea c\u003c/sup\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eImmunocompromised\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e24 (46.15)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e10 (55.56)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e14 (41.18)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003e0.388\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eSepsis\u003cstrong\u003e\u003csup\u003e\u0026nbsp;d\u003c/sup\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e19 (34.55)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e4 (22.22)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e15 (40.54)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003e0.234\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eLiving with HIV\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e16 (30.77)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e9 (50.0)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e7 (20.59)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003e0.056\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003ePersons Who Inject Drugs \u003cstrong\u003e\u003csup\u003ee\u003c/sup\u003e\u003c/strong\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e13 (29.55)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e10 (62.50)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e3 (10.71)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003e0.001*\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eHepatitis C\u003cstrong\u003e\u003csup\u003e\u0026nbsp;\u003c/sup\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e9 (17.31)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e7 (38.89)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e2 (5.88)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003e0.005*\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003ePneumonia\u003cstrong\u003e\u003csup\u003e\u0026nbsp;\u003c/sup\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e8 (15.38)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e2 (11.11)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e6 (17.65)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003e0.698\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eKidney Injury or Disease\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e8 (15.38)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e2 (11.11)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e6 (17.65)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003e0.698\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eRenal Failure\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e5 (9.62)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e5 (14.71)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003e0.150\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eHypertension\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e5 (9.62)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e1 (5.56)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e4 (11.76)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003e0.648\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 180px;\"\u003e\n \u003cp\u003eNosocomial Infection \u003cstrong\u003e\u003csup\u003ef\u003c/sup\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 96px;\"\u003e\n \u003cp\u003e4 (7.55)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 102px;\"\u003e\n \u003cp\u003e0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e4 (11.43)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 132px;\"\u003e\n \u003cp\u003e0.287\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u003cstrong\u003eAbbreviations: \u0026nbsp;\u0026nbsp;\u003c/strong\u003e\u003cem\u003eNA\u003c/em\u003e \u0026ndash; Not applicable; \u003cem\u003eHIV\u0026nbsp;\u003c/em\u003e\u0026ndash; Human immunodeficiency virus\u003c/p\u003e\n\u003cp\u003eP \u0026lt; 0.05 was considered statistically significant\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e*\u003c/strong\u003e\u0026nbsp; \u0026nbsp;Statistically significant observation\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003csup\u003ea\u003c/sup\u003e\u003c/strong\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp;Section had a diverging number of data points due to missing patient information\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003csup\u003eb\u003c/sup\u003e\u003c/strong\u003e\u0026nbsp; \u0026nbsp; Hospital bed capacity: Hospital 1 \u0026ndash; 845 beds; Hospital 2 \u0026ndash; 840 beds; Hospital 3 \u0026ndash; 44 beds; Hospital 4 \u0026ndash; 857\u0026nbsp;\u003cbr\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;beds; Hospital 5 \u0026ndash; 202 beds; Hospital 6 \u0026ndash; 153 beds; Hospital 7 \u0026ndash; 325 beds.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003csup\u003ec\u003c/sup\u003e\u003c/strong\u003e\u0026nbsp; \u0026nbsp; Data in this sub-section was available for 52 patients (34 SAB, 18 SAIE) unless stated otherwise; deviations\u0026nbsp;\u003cbr\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;from this baseline are indicated per characteristic.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003csup\u003ed - f\u003c/sup\u003e\u003c/strong\u003e Data was available for \u003cstrong\u003e\u003csup\u003ed\u003c/sup\u003e\u003c/strong\u003e 55 patients (37 SAB, 18 SAIE),\u003cstrong\u003e\u003csup\u003e\u0026nbsp;\u003c/sup\u003e\u003c/strong\u003e\u003cstrong\u003e\u003csup\u003ee\u003c/sup\u003e\u003c/strong\u003e 44 patients (28 SAB, 16 SAIE) and\u003cstrong\u003e\u003csup\u003e\u0026nbsp;f\u0026nbsp;\u003c/sup\u003e\u003c/strong\u003e53 patients\u0026nbsp;\u003cbr\u003e\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; (35 SAB, 18 SAIE)\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTable 2: Logistic regression analysis of potential predictor variables in \u003cem\u003eStaphylococcus aureus\u003c/em\u003e infective endocarditis development\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"606\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 258px;\"\u003e\n \u003cp\u003e\u003cstrong\u003ePredictor Variable\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eOdds Ratio\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e\u003cstrong\u003e95% Confidence Interval\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eP-value\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 258px;\"\u003e\n \u003cp\u003eIntravenous drug use\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e7.46\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e1.24 - 45.05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e0.028*\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 258px;\"\u003e\n \u003cp\u003eHIV status\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e2.15\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e0.42 - 10.96\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e0.357\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 258px;\"\u003e\n \u003cp\u003eHepatitis C\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e3.60\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e0.45 - 28.96\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e0.229\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 258px;\"\u003e\n \u003cp\u003eIntercept (Baseline Odds)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e0.17\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e0.05 - 0.50\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 116px;\"\u003e\n \u003cp\u003e0.002*\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u003cstrong\u003eAbbreviations: \u0026nbsp;\u0026nbsp;\u003c/strong\u003e\u003cem\u003eHIV\u0026nbsp;\u003c/em\u003e\u0026ndash; Human immunodeficiency virus\u003c/p\u003e\n\u003cp\u003eP \u0026lt; 0.05 was considered statistically significant.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e*\u003c/strong\u003e\u0026nbsp; \u0026nbsp;Statistically significant observation\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTable 3: Biofilm formation capabilities of the \u003cem\u003eStaphylococcus aureus\u003c/em\u003e bacteraemia and infective endocarditis isolates\u003c/strong\u003e\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"605\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"3\" style=\"width: 78px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eBiofilm Formation Capability\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"3\" style=\"width: 126px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eNo. of Isolates with the Biofilm Formation Capability\u0026nbsp;\u003cbr\u003e\u0026nbsp;[n = 77 (%)]\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"4\" style=\"width: 345px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eNo. of Isolates with the Biofilm Formation Capability by Infection Type [n (%)]\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"3\" style=\"width: 57px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eP value\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"2\" style=\"width: 174px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eInfective Endocarditis\u0026nbsp;\u003cbr\u003e\u0026nbsp;(n = 23)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width: 171px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eBacteraemia (n = 54)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 86px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMean OD (Range)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 88px;\"\u003e\n \u003cp\u003e\u003cstrong\u003en (%)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 85px;\"\u003e\n \u003cp\u003e\u003cstrong\u003eMean OD (Range)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 86px;\"\u003e\n \u003cp\u003e\u003cstrong\u003en (%)\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003eNon\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 126px;\"\u003e\n \u003cp\u003e8 (10.39)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 86px;\"\u003e\n \u003cp\u003e0.12 (0.04 \u0026ndash; 0.19)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 88px;\"\u003e\n \u003cp\u003e2 (8.70)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 85px;\"\u003e\n \u003cp\u003e0.19 (0.17 \u0026ndash; 0.20)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 86px;\"\u003e\n \u003cp\u003e6 (11.11)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 57px;\"\u003e\n \u003cp\u003e1.000\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003eWeak\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 126px;\"\u003e\n \u003cp\u003e19 (24.68)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 86px;\"\u003e\n \u003cp\u003e0.26 (0.22 - 0.31)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 88px;\"\u003e\n \u003cp\u003e5 (21.74)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 85px;\"\u003e\n \u003cp\u003e0.26 (0.21 \u0026ndash; 0.31)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 86px;\"\u003e\n \u003cp\u003e14 (25.93)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 57px;\"\u003e\n \u003cp\u003e0.780\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003eModerate\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 126px;\"\u003e\n \u003cp\u003e20 (25.97)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 86px;\"\u003e\n \u003cp\u003e0.36 (0.34 \u0026ndash; 0.41)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 88px;\"\u003e\n \u003cp\u003e4 (17.39)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 85px;\"\u003e\n \u003cp\u003e0.41 (0.34 \u0026ndash; 0.49)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 86px;\"\u003e\n \u003cp\u003e16 (29.63)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 57px;\"\u003e\n \u003cp\u003e0.395\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003eStrong\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 126px;\"\u003e\n \u003cp\u003e30 (38.96)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 86px;\"\u003e\n \u003cp\u003e1.03 (0.52 - 2.40)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 88px;\"\u003e\n \u003cp\u003e12 (52.17)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 85px;\"\u003e\n \u003cp\u003e0.85 (0.53 \u0026ndash; 1.36)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 86px;\"\u003e\n \u003cp\u003e18 (33.33)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 57px;\"\u003e\n \u003cp\u003e0.134\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u003cstrong\u003eAbbreviations: \u0026nbsp;\u0026nbsp;\u003c/strong\u003e\u003cem\u003eOD\u0026nbsp;\u003c/em\u003e\u0026ndash; Optical density\u003c/p\u003e\n\u003cp\u003eP \u0026lt; 0.05 was considered statistically significant.\u003c/p\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"world-journal-of-microbiology-and-biotechnology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"wibi","sideBox":"Learn more about [World Journal of Microbiology and Biotechnology](https://www.springer.com/journal/11274)","snPcode":"11274","submissionUrl":"https://submission.nature.com/new-submission/11274/3","title":"World Journal of Microbiology and Biotechnology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"bacteraemia, genetic relatedness, infective endocarditis, Staphylococcus aureus, virulence","lastPublishedDoi":"10.21203/rs.3.rs-8678564/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8678564/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cem\u003eStaphylococcus aureus\u003c/em\u003e (\u003cem\u003eS. aureus\u003c/em\u003e) is a leading cause of bacteraemia and infective endocarditis worldwide, posing significant public health challenges in resource-limited low- and middle-income countries (LMICs). However, whether specific genomic factors influence \u003cem\u003eS. aureus\u003c/em\u003e infective endocarditis (SAIE) development during \u003cem\u003eS. aureus\u003c/em\u003e bacteraemia (SAB) remains unclear. Thus, the study aimed to determine whether clinical SAIE isolates were genomically distinguishable from SAB isolates originating from public hospitals in Gauteng, South Africa. Seventy-seven (54 SAB, 23 SAIE) bloodstream isolates were characterised to assess antimicrobial susceptibility (VITEK\u003csup\u003e®\u003c/sup\u003e2 system), biofilm formation (crystal violet assay), virulence genes (multiplex-polymerase chain reactions) and genetic relatedness (pulsed-field gel electrophoresis). Twelve representative isolates underwent whole-genome sequencing to assess their mobilome, resistome, virulome and phylogenetic relatedness. A higher SAIE (29.9%) prevalence than previously reported in South Africa was observed, with cases linked to young male persons who inject drugs (P \u0026lt; 0.01). While SAB and SAIE groups did not differ in virulence profiles, SAB cases demonstrated higher resistance rates to gentamicin and clindamycin compared to SAIE (P \u0026lt; 0.05). The endemic Panton-Valentine leukocidin-positive sequence-type (ST) 152, clonal-complex (CC) 152 lineage predominated in SAIE isolates, while the pandemic CC8, encompassing ST239, ST508 and ST612, was exclusive to SAB isolates. The findings suggest that all SAB isolates may be capable of progressing to more severe SAIE forms with host risk factors as key predictors. Circulation of diverse, highly pathogenic \u003cem\u003eS. aureus\u003c/em\u003e strains highlights the need for surveillance and targeted infection control.\u003c/p\u003e","manuscriptTitle":"Genomic comparison of Staphylococcus aureus isolates from patients with bacteraemia and infective endocarditis at public hospitals in Gauteng, South Africa","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-02-16 10:34:23","doi":"10.21203/rs.3.rs-8678564/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-05-04T14:38:48+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-04-17T12:41:06+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-04-16T22:37:50+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"154155397815182070888485416396722780903","date":"2026-03-19T16:42:47+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"92687415831610746804956321096029151525","date":"2026-03-19T08:50:14+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-02-11T09:16:58+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-01-27T12:35:33+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-01-27T11:43:07+00:00","index":"","fulltext":""},{"type":"submitted","content":"World Journal of Microbiology and Biotechnology","date":"2026-01-23T10:57:25+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"world-journal-of-microbiology-and-biotechnology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"wibi","sideBox":"Learn more about [World Journal of Microbiology and Biotechnology](https://www.springer.com/journal/11274)","snPcode":"11274","submissionUrl":"https://submission.nature.com/new-submission/11274/3","title":"World Journal of Microbiology and Biotechnology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"a3f5dcd3-0e26-426c-935d-72a17bdfae40","owner":[],"postedDate":"February 16th, 2026","published":true,"recentEditorialEvents":[{"type":"decision","content":"Revision requested","date":"2026-05-04T14:38:48+00:00","index":"","fulltext":""}],"rejectedJournal":[],"revision":"","amendment":"","status":"in-revision","subjectAreas":[],"tags":[],"updatedAt":"2026-05-04T14:54:51+00:00","versionOfRecord":[],"versionCreatedAt":"2026-02-16 10:34:23","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8678564","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8678564","identity":"rs-8678564","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}